Introduction

MaAsLin 3 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).

MaAsLin3 is comprehensive R package for efficiently determining multivariable associations between clinical metadata and microbial meta-omics features. Relative to MaAsLin 2, MaAsLin 3 introduces the ability to quantify and test for both abundance and prevalence associations while accounting for compositionality. MaAsLin3 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, along with a variety of filtering, normalization, and transform methods.

If you use the MaAsLin 3 software, please cite our manuscript:

William A. Nickols, Jacob T. Nearing, Kelsey N. Thompson, Jiaxian Shen, Curtis Huttenhower MaAsLin 3: Refining and extending generalized multivariate linear models for meta-omic association discovery. (In progress).

Support

If you have questions, please direct it to: MaAsLin 3 Forum .

Contents

1. Installing R

R is a programming language specializing in statistical computing and graphics. You can use R just the same as any other programming languages, but it is most useful for statistical analyses, with well-established packages for common tasks such as linear modeling, ’omic data analysis, machine learning, and visualization. We have created a short introduction tutorial here, but we note there are many other more comprehensive tutorials out there to learn R.

Installing R for the first time

You can download and install the free R software environment here. Note that you should download the latest release - this will ensure the R version you have is compatible with MaAsLin 3.

(Optional) the RStudio IDE

RStudio is a freely available IDE (integrated development environment) for R. It is a “wrapper” around R with some additional functionalities that makes programming in R a bit easier. Feel free to download RStudio and explore its interface - but it is not required for this tutorial.

Important: the correct R version

If you already have R installed, then it is possible that the R version you have does not support MaAsLin 3. The easiest way to check this is to launch R/RStudio, and in the console (“Console” pane in RStudio), type in the following command (without the > symbol):

sessionInfo()

The first line of output message should indicate your current R version. For example:

> sessionInfo()
R version 4.4.1 (2024-06-14)

For MaAsLin 3 to install, you will need R >= 4.3. If your version is older than that, please refer to section Installing R for the first time to download the latest R. Note that RStudio users will need to have RStudio “switch” to this later version once it is installed. This should happen automatically for Windows and Mac OS users when you relaunch RStudio. For Linux users you might need to bind the correct R executable. For more information refer to here. Either way, once you have the correct version installed, launch the software and use sessionInfo() to make sure that you indeed have R >= 4.3.

2. Installing MaAsLin 3

The latest development version of MaAsLin 3 can be installed from GitHub using the devtools package.

if (!require('devtools', character.only = TRUE)) {
  install.packages('devtools')
}

library("devtools")
install_github("biobakery/MaAsLin3")
for (lib in c('maaslin3', 'dplyr', 'ggplot2', 'knitr', 'kableExtra')) {
    suppressPackageStartupMessages(require(lib, character.only = TRUE))
}

3. Microbiome Association Detection with MaAsLin 3

To run MaAsLin 3, a user inputs a table of per-sample feature abundances (with zeros still included), a table of per-sample metadata, and a model specifying how the metadata should relate to the feature presence/absence and abundance. MaAsLin 3 will return a table of associations including an effect size and p-value for each feature-metadatum association and a folder of visuals including a summary plot and diagnostic plots for significant associations.

3.1 MaAsLin 3 Input

MaAsLin3 requires two input files.

  1. Feature abundance data frame
    • Formatted with features as columns and samples as rows.
    • The transpose of this format is also okay.
    • Possible features in this file include taxonomy or genes. These can be relative abundances or counts.
    • This can be a filepath to a tab-delimited file.
  2. Metadata data frame
    • Formatted with variables as columns and samples as rows.
    • The transpose of this format is also okay.
    • Possible metadata in this file include gender or age.
    • This can be a filepath to a tab-delimited file.

The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.

Example input files can be found in the inst/extdata folder of the MaAsLin 3 source. The files provided were generated from the HMP2 data which can be downloaded from https://ibdmdb.org/ .

# Read abundance table
taxa_table_name <- system.file("extdata", "HMP2_taxonomy.tsv", package = "maaslin3")
taxa_table <- read.csv(taxa_table_name, sep = '\t')

# Read metadata table
metadata_name <- system.file("extdata", "HMP2_metadata.tsv", package = "maaslin3")
metadata <- read.csv(metadata_name, sep = '\t')

# Factor the categorical variables to test against controls
metadata$diagnosis <- 
  factor(metadata$diagnosis, levels = c('nonIBD', 'UC', 'CD'))
metadata$dysbiosis_state <- 
  factor(metadata$dysbiosis_state, levels = c('none', 'dysbiosis_UC', 'dysbiosis_CD'))
metadata$antibiotics <- 
  factor(metadata$antibiotics, levels = c('No', 'Yes'))

taxa_table[1:5, 1:5]
##            Phocaeicola_vulgatus Faecalibacterium_prausnitzii
## CSM5FZ3N_P            0.4265226                  0.060255109
## CSM5FZ3R_P            0.5369584                  0.007396904
## CSM5FZ3T_P            0.5911821                  0.000000000
## CSM5FZ3V_P            0.2661378                  0.029680329
## CSM5FZ3X_P            0.6601039                  0.003596740
##            Bacteroides_uniformis Prevotella_copri_clade_A Bacteroides_stercoris
## CSM5FZ3N_P          0.2692411314             0.000000e+00           0.000000000
## CSM5FZ3R_P          0.2526048469             0.000000e+00           0.008390958
## CSM5FZ3T_P          0.0000000000             0.000000e+00           0.000000000
## CSM5FZ3V_P          0.4004265260             0.000000e+00           0.000000000
## CSM5FZ3X_P          0.0008804283             1.308102e-05           0.001335669
metadata[1:5, 1:5]
##            participant_id    site_name week_num    reads diagnosis
## CSM5FZ3N_P          C3001 Cedars-Sinai        0  9961743        CD
## CSM5FZ3R_P          C3001 Cedars-Sinai        2 16456391        CD
## CSM5FZ3T_P          C3002 Cedars-Sinai        0 10511448        CD
## CSM5FZ3V_P          C3001 Cedars-Sinai        6 17808965        CD
## CSM5FZ3X_P          C3002 Cedars-Sinai        2 13160893        CD

HMP2_taxonomy.tsv: is a tab-delimited file with samples as rows and species as columns. It is a subset of the taxonomy file that includes just some of the the species abundances.

HMP2_metadata.tsv: is a tab-delimited file with samples as rows and metadata as columns. It is a subset of the metadata file that includes just some of the fields.

3.2 Running MaAsLin 3

MaAsLin 3 is run by specifying a param_list that contains the abundance table (input_data), the metadata table (input_metadata), the output directory (output), and a model specification. The model specification can come from a formula or vectors of terms. In either case, variable names should not have spaces or unusual characters.

  • Formula: The formula parameter should be set to any formula that satisfies the lme4 specifications: fixed effects, interaction terms, random effects, polynomial terms, and more can all be included. In addition, group and ordered predictors (see below) can be included by including group(variable_name) and ordered(variable_name) in the formula.
  • Vectors: Alternatively, a vector of variables can be supplied to the parameters fixed_effects, random_effects, group_effects, and ordered_effects. Categorical variables should either be ordered as factors beforehand, or reference should be provided as a string of ‘variable,reference’ semi-colon delimited for multiple variables (e.g., variable_1,reference_1;variable_2,reference_2). NOTE: adding a space between the variable and level might result in the wrong reference level being used.

Because MaAsLin 3 considers prevalence associations, read depth (number of reads) should be included as a covariate if available since deeper sequencing will likely increase feature detection in a way that could spuriously correlate with metadata of interest.

Running MaAsLin 3 on HMP2 data

The following command runs MaAsLin 3 on the HMP2 data, running a multivariable regression model to test for the association between microbial species abundance and prevalence versus IBD diagnosis and dysbiosis scores while controlling for antibiotic usage, age, and the sampling depth (reads). Outputs are generated in a folder called demo_output under the current working directory (output = "demo_output").

To show one of each type of plot (see below), the maximum number of significant associations to plot has been increased with max_pngs=100. All other parameters beyond the first four are the default parameters but are still included for clarity. By default, total sum scaling with a log transformation afterwards will be used. However, other normalizations and transformations are allowed (see normalization and transform in the manual). Also by default, a data augmentation procedure is used to avoid linear separability in the logistic regressions. This is almost always recommended, though it can be turned off (see augment in the manual). A nominal FDR level of 0.1 determines which associations are significant, but this can also be changed (see max_significance in the manual). For the abundance coefficients, to account for compositionality in relative abundance data, significance is determined by comparing against the median coefficient for a metadatum across the features (median_comparison_abundance). Since prevalence coefficients do not have the same compositional properties, they are instead compared against 0 (median_comparison_prevalence). See the manual for a discussion of when to change these parameters. One CPU is used for fitting (cores = 1).

param_list <- list(input_data = taxa_table, 
                   input_metadata = metadata, 
                   output = 'demo_output', 
                   formula = '~ diagnosis + dysbiosis_state + antibiotics + age + reads',
                   normalization = 'TSS', 
                   transform = 'LOG', 
                   augment = TRUE, 
                   max_significance = 0.1, 
                   median_comparison_abundance = TRUE, 
                   median_comparison_prevalence = FALSE, 
                   max_pngs = 100,
                   cores = 1)

fit_out <- maaslin3(param_list)

Median comparisons

When median_comparison_abundance or median_comparison_prevalence are on, the coefficients for a metadatum will be tested against the median coefficient for that metadatum (median across the features). Otherwise, the coefficients will be tested against 0. For abundance associations, this is designed to account for compositionality, the idea that if only one feature has a positive association with a metadatum on the absolute scale, the other features will have apparent negative associations with that metadatum on the relative scale because relative abundances must sum to 1. More generally, associations on the relative scale are not necessarily the same as the associations on the absolute scale in magnitude or sign, so testing against zero on the relative scale is not equivalent to testing against zero on absolute scale. However, the median comparison enables some inference on the absolute scale. There are two interpretations of this test for absolute abundance associations:

  1. In linear models, if two features’ associations with a particular metadatum on the log absolute scale differ by some value \(d\), the features’ associations with that metadatum on the log relative scale (total-sum scaling) will also differ by \(d\). Therefore, the test against the median can always be interpreted as a test of whether a particular association is significantly different from the typical association on the absolute scale. (Or, equivalently because of the 1-1 relation, this tests whether a particular association is significantly different from the typical association on the relative scale).
  2. Under the assumption that at least half the features are not changing on the absolute scale, the median true absolute coefficient is 0, so this can be interpreted as a test of whether the feature has a non-zero association on the absolute scale

By contrast, sparsity should be less affected by compositionality since a feature should still be present even if another increases or decreases in abundance. (However, because the read depth is finite, this might not perfectly hold.) Therefore, median_comparison_prevalence is off by default, but it can be turned on if the user is interested in testing whether a particular prevalence association is significantly different from the typical prevalence association.

In both cases, if the tested coefficient is within median_comparison_[abundance/prevalence]_threshold of the median, it will automatically receive a p-value of 1. This is based on the idea that the association might be statistically significantly different but not substantially different from the median and therefore is likely still a compositional effect.

To conclude:

  • median_comparison_abundance is TRUE by default and should be used to make inference on the absolute scale when using relative abundance data.
  • median_comparison_abundance should be FALSE when (1) testing for significant relative associations, (2) testing for absolute abundance associations under the assumption that the total absolute abundance is not changing, or (3) testing for significant absolute associations when supplying spike-in or total abundances with unscaled_abundance.
  • median_comparison_prevalence is FALSE by default since most analysis focuses on whether a prevalence association is non-zero, not whether it is significantly different from the typical prevalence association.

3.3 MaAsLin 3 Output

Significant associations

The main output from MaAsLin 3 is the list of significant associations in significant_results.tsv. This lists all associations that pass MaAsLin 3’s significance threshold, ordered by increasing joint q-value. The format is:

  • Columns 1 and 2 are the feature and metadata names.
  • Columns 3 and 4 are the value of the metadata and variable name from the model.
  • Columns 5 and 6 are the fit coefficient and standard error from the model.
  • Columns 7 and 8 are the p-value and FDR corrected q-value of the individual association.
  • Column 9 species whether the association is abundance or prevalence.
  • Column 10 is the total number of data points.
  • Column 11 is the total number of non-zero data points.
  • Columns 12 and 13 are the p-value and q-value of the joint prevalence and abundance association.
feature metadata value name coef stderr pval_individual qval_individual model N N.not.zero pval_joint qval_joint
Escherichia_coli dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 3.53 0.387 0 0 abundance 1530 707 0 0
Veillonella_parvula dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 4.05 0.488 0 0 abundance 1530 547 0 0
Escherichia_coli dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.58 0.237 2.57e-11 2.92e-10 prevalence 1530 707 0 0
Veillonella_parvula dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.852 0.215 7.22e-05 0.000245 prevalence 1530 547 0 0
Phocaeicola_sartorii reads reads reads -0.24 0.148 1 1 abundance 1530 424 1.08e-43 3.82e-41
Phocaeicola_sartorii reads reads reads 1.1 0.0787 5.42e-44 5.73e-41 prevalence 1530 424 1.08e-43 3.82e-41
Faecalibacterium_prausnitzii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.18 0.309 2.91e-10 1.64e-08 abundance 1530 1370 7.09e-35 1.87e-32
Faecalibacterium_prausnitzii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.49 0.282 3.54e-35 1.87e-32 prevalence 1530 1370 7.09e-35 1.87e-32
Bacteroides_uniformis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.12 0.396 3.99e-13 3.99e-11 abundance 1530 1240 3.15e-31 6.66e-29
Bacteroides_uniformis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.91 0.249 1.58e-31 5.55e-29 prevalence 1530 1240 3.15e-31 6.66e-29
Bifidobacterium_longum age age age -0.129 0.106 1 1 abundance 1530 843 2.02e-29 3.56e-27
Bifidobacterium_longum age age age -0.672 0.0594 1.01e-29 2.67e-27 prevalence 1530 843 2.02e-29 3.56e-27
Clostridium_sp_AM49_4BH diagnosis CD diagnosisCD -0.68 0.344 0.0769 0.188 abundance 1530 344 2.22e-28 3.36e-26
Clostridium_sp_AM49_4BH diagnosis CD diagnosisCD -1.81 0.163 1.11e-28 2.35e-26 prevalence 1530 344 2.22e-28 3.36e-26
Phocaeicola_dorei reads reads reads -0.519 0.197 1 1 abundance 1530 769 5.13e-25 6.77e-23
Phocaeicola_dorei reads reads reads 0.66 0.0634 2.56e-25 4.51e-23 prevalence 1530 769 5.13e-25 6.77e-23
GGB16040_SGB9347 age age age -0.378 0.297 0.219 0.421 abundance 1530 114 5.29e-24 6.21e-22
GGB16040_SGB9347 age age age 0.96 0.0944 2.65e-24 4e-22 prevalence 1530 114 5.29e-24 6.21e-22
Firmicutes_bacterium_AF16_15 diagnosis UC diagnosisUC -0.47 0.246 0.0275 0.084 abundance 1530 827 1.35e-23 1.43e-21
Firmicutes_bacterium_AF16_15 diagnosis UC diagnosisUC -1.67 0.166 6.77e-24 8.95e-22 prevalence 1530 827 1.35e-23 1.43e-21
Eubacterium_rectale dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.602 0.386 0.321 0.557 abundance 1530 1210 4.94e-23 4.74e-21
Eubacterium_rectale dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.36 0.237 2.47e-23 2.9e-21 prevalence 1530 1210 4.94e-23 4.74e-21
Phascolarctobacterium_faecium age age age 0.186 0.104 1 1 abundance 1530 503 6.39e-23 5.63e-21
Phascolarctobacterium_faecium age age age 0.574 0.0578 3.19e-23 3.38e-21 prevalence 1530 503 6.39e-23 5.63e-21
Dysosmobacter_welbionis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.7 0.342 0.00732 0.0295 abundance 1530 1190 7.38e-23 6e-21
Dysosmobacter_welbionis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.4 0.242 3.69e-23 3.55e-21 prevalence 1530 1190 7.38e-23 6e-21
Blautia_faecis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.03 0.474 0.00846 0.0334 abundance 1530 1120 5.31e-22 4.01e-20
Blautia_faecis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.42 0.249 2.66e-22 2.34e-20 prevalence 1530 1120 5.31e-22 4.01e-20
Fusicatenibacter_saccharivorans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.311 0.4 0.186 0.375 abundance 1530 1120 9.03e-22 6.37e-20
Fusicatenibacter_saccharivorans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.35 0.243 4.52e-22 3.67e-20 prevalence 1530 1120 9.03e-22 6.37e-20
Prevotella_sp_885 age age age 1.28 0.566 0.0261 0.0803 abundance 1530 69 2.48e-21 1.64e-19
Prevotella_sp_885 age age age 1.13 0.118 1.24e-21 9.37e-20 prevalence 1530 69 2.48e-21 1.64e-19
Lachnospira_sp_NSJ_43 diagnosis CD diagnosisCD -0.403 0.401 0.406 0.662 abundance 1530 296 1.79e-20 1.11e-18
Lachnospira_sp_NSJ_43 diagnosis CD diagnosisCD -1.65 0.177 8.94e-21 6.3e-19 prevalence 1530 296 1.79e-20 1.11e-18
Bacteroides_ovatus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.278 0.429 0.248 0.456 abundance 1530 1180 2.18e-20 1.28e-18
Bacteroides_ovatus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.13 0.228 1.09e-20 7.21e-19 prevalence 1530 1180 2.18e-20 1.28e-18
Clostridium_sp_AM49_4BH diagnosis UC diagnosisUC 0.136 0.357 1 1 abundance 1530 344 5.02e-20 2.79e-18
Clostridium_sp_AM49_4BH diagnosis UC diagnosisUC -1.57 0.17 2.51e-20 1.56e-18 prevalence 1530 344 5.02e-20 2.79e-18
Bacteroides_faecis reads reads reads -0.841 0.177 0.00513 0.0221 abundance 1530 434 1.49e-19 7.88e-18
Bacteroides_faecis reads reads reads 0.6 0.0657 7.46e-20 4.38e-18 prevalence 1530 434 1.49e-19 7.88e-18
Phocaeicola_vulgatus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.59 0.507 3.26e-06 5.35e-05 abundance 1530 1290 1.74e-19 8.74e-18
Phocaeicola_vulgatus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.07 0.228 8.68e-20 4.83e-18 prevalence 1530 1290 1.74e-19 8.74e-18
Dysosmobacter_welbionis reads reads reads -0.207 0.0627 1 1 abundance 1530 1190 4.2e-19 2.02e-17
Dysosmobacter_welbionis reads reads reads 0.719 0.0798 2.1e-19 1.11e-17 prevalence 1530 1190 4.2e-19 2.02e-17
Roseburia_sp_AF02_12 diagnosis CD diagnosisCD 0.519 0.382 0.125 0.277 abundance 1530 363 4.87e-19 2.24e-17
Roseburia_sp_AF02_12 diagnosis CD diagnosisCD -1.38 0.154 2.44e-19 1.23e-17 prevalence 1530 363 4.87e-19 2.24e-17
Clostridiales_bacterium dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.03 0.557 0.0252 0.0796 abundance 1530 985 7.12e-19 3.14e-17
Clostridiales_bacterium dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.46 0.275 3.56e-19 1.71e-17 prevalence 1530 985 7.12e-19 3.14e-17
Alistipes_putredinis diagnosis UC diagnosisUC -1.4 0.225 8.37e-11 5.79e-09 abundance 1530 873 1.01e-18 4.28e-17
Alistipes_putredinis diagnosis UC diagnosisUC -1.42 0.159 5.06e-19 2.33e-17 prevalence 1530 873 1.01e-18 4.28e-17
Bacteroides_xylanisolvens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.81 0.691 0.000185 0.00145 abundance 1530 959 1.06e-18 4.3e-17
Bacteroides_xylanisolvens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.12 0.238 5.29e-19 2.33e-17 prevalence 1530 959 1.06e-18 4.3e-17
Parabacteroides_distasonis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.119 0.334 1 1 abundance 1530 1140 1.62e-18 6.33e-17
Parabacteroides_distasonis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.99 0.225 8.09e-19 3.42e-17 prevalence 1530 1140 1.62e-18 6.33e-17
Clostridium_sp_AT4 diagnosis UC diagnosisUC 0.939 0.31 0.00541 0.0231 abundance 1530 528 2.99e-18 1.13e-16
Clostridium_sp_AT4 diagnosis UC diagnosisUC 1.41 0.161 1.5e-18 6.08e-17 prevalence 1530 528 2.99e-18 1.13e-16
Gemmiger_formicilis diagnosis UC diagnosisUC 1.41 0.36 0.000217 0.00164 abundance 1530 472 3.29e-18 1.2e-16
Gemmiger_formicilis diagnosis UC diagnosisUC -1.45 0.165 1.65e-18 6.44e-17 prevalence 1530 472 3.29e-18 1.2e-16
Coprococcus_eutactus age age age -0.172 0.204 1 1 abundance 1530 177 3.81e-18 1.34e-16
Coprococcus_eutactus age age age 0.649 0.0741 1.91e-18 7.2e-17 prevalence 1530 177 3.81e-18 1.34e-16
Alistipes_SGB2313 age age age 1.01 0.302 0.00116 0.0067 abundance 1530 73 4.82e-18 1.64e-16
Alistipes_SGB2313 age age age 0.949 0.109 2.41e-18 8.78e-17 prevalence 1530 73 4.82e-18 1.64e-16
GGB1549_SGB2133 age age age 2.2 0.5 7.68e-05 0.000692 abundance 1530 46 9.43e-18 3.12e-16
Vescimonas_coprocola diagnosis CD diagnosisCD 0.426 0.23 0.0318 0.0929 abundance 1530 599 1.21e-17 3.86e-16
Vescimonas_coprocola diagnosis CD diagnosisCD -1.2 0.139 6.03e-18 2.06e-16 prevalence 1530 599 1.21e-17 3.86e-16
Clostridium_fessum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.66 0.603 0.0172 0.0575 abundance 1530 926 1.34e-17 4.17e-16
Clostridium_fessum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.66 0.309 6.71e-18 2.22e-16 prevalence 1530 926 1.34e-17 4.17e-16
Bacteroides_thetaiotaomicron dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.592 0.549 0.14 0.299 abundance 1530 1060 1.66e-17 5.02e-16
Bacteroides_thetaiotaomicron dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.06 0.239 8.31e-18 2.66e-16 prevalence 1530 1060 1.66e-17 5.02e-16
Lacrimispora_amygdalina age age age -0.331 0.0802 7.15e-05 0.000657 abundance 1530 865 3.54e-17 1.04e-15
Lacrimispora_amygdalina age age age -0.491 0.0577 1.77e-17 5.5e-16 prevalence 1530 865 3.54e-17 1.04e-15
GGB9342_SGB14306 age age age 0.804 0.0958 4.87e-17 1.35e-15 prevalence 1530 92 4.87e-17 1.39e-15
Alistipes_putredinis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.33 0.577 9.33e-08 2.71e-06 abundance 1530 873 5.18e-17 1.44e-15
Alistipes_putredinis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.34 0.276 2.59e-17 7.82e-16 prevalence 1530 873 5.18e-17 1.44e-15
Anaerostipes_hadrus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.026 0.41 1 1 abundance 1530 1130 5.89e-17 1.56e-15
Bacteroides_intestinalis age age age 0.592 0.221 0.00727 0.0295 abundance 1530 158 5.78e-17 1.56e-15
Anaerostipes_hadrus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2 0.237 2.94e-17 8.41e-16 prevalence 1530 1130 5.89e-17 1.56e-15
Bacteroides_intestinalis age age age 0.667 0.079 2.89e-17 8.41e-16 prevalence 1530 158 5.78e-17 1.56e-15
Bacteroides_cellulosilyticus age age age 0.675 0.158 1.72e-05 0.000204 abundance 1530 433 1.21e-16 3.12e-15
Bacteroides_cellulosilyticus age age age 0.483 0.0578 6.04e-17 1.64e-15 prevalence 1530 433 1.21e-16 3.12e-15
Candidatus_Cibionibacter_quicibialis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.551 0.54 0.155 0.324 abundance 1530 933 1.43e-16 3.59e-15
Candidatus_Cibionibacter_quicibialis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.09 0.25 7.14e-17 1.89e-15 prevalence 1530 933 1.43e-16 3.59e-15
Bacteroides_eggerthii reads reads reads -1.02 0.225 0.00288 0.0139 abundance 1530 409 2.79e-16 6.85e-15
Bacteroides_eggerthii reads reads reads 0.552 0.0668 1.39e-16 3.59e-15 prevalence 1530 409 2.79e-16 6.85e-15
Veillonella_dispar age age age -0.203 0.163 1 1 abundance 1530 526 4.49e-16 1.08e-14
Veillonella_dispar age age age -0.527 0.0642 2.25e-16 5.65e-15 prevalence 1530 526 4.49e-16 1.08e-14
Haemophilus_parainfluenzae age age age -0.22 0.117 1 1 abundance 1530 674 6.58e-16 1.55e-14
Haemophilus_parainfluenzae age age age -0.473 0.058 3.29e-16 8.09e-15 prevalence 1530 674 6.58e-16 1.55e-14
Faecalibacterium_prausnitzii age age age -0.442 0.0524 4.44e-16 1.33e-13 abundance 1530 1370 8.88e-16 2.04e-14
Faecalibacterium_prausnitzii age age age -0.56 0.103 5.4e-08 3.3e-07 prevalence 1530 1370 8.88e-16 2.04e-14
Bacteroides_caccae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.25 0.424 0.0157 0.0543 abundance 1530 958 1.46e-15 3.28e-14
Bacteroides_caccae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.92 0.238 7.28e-16 1.75e-14 prevalence 1530 958 1.46e-15 3.28e-14
Clostridium_sp_AF34_10BH dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.586 0.68 0.237 0.442 abundance 1530 960 1.64e-15 3.61e-14
Clostridium_sp_AF34_10BH dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.33 0.289 8.19e-16 1.92e-14 prevalence 1530 960 1.64e-15 3.61e-14
Flavonifractor_plautii reads reads reads -0.287 0.0722 1 1 abundance 1530 1220 3.2e-15 6.91e-14
Flavonifractor_plautii reads reads reads 0.611 0.0766 1.6e-15 3.68e-14 prevalence 1530 1220 3.2e-15 6.91e-14
Enterocloster_bolteae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.75 0.366 1.67e-15 3.75e-13 abundance 1530 866 3.33e-15 7.04e-14
Enterocloster_bolteae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.133 0.209 0.525 0.62 prevalence 1530 866 3.33e-15 7.04e-14
Bacteroides_ovatus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.58 0.745 0.114 0.256 abundance 1530 1180 9e-15 1.83e-13
Ruminococcus_gnavus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.52 0.341 4.44e-15 7.99e-13 abundance 1530 767 8.88e-15 1.83e-13
Bacteroides_ovatus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.97 0.379 4.5e-15 1.01e-13 prevalence 1530 1180 9e-15 1.83e-13
Ruminococcus_gnavus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.01 0.225 8.05e-06 3.44e-05 prevalence 1530 767 8.88e-15 1.83e-13
Bacteroides_xylanisolvens diagnosis UC diagnosisUC -2.51 0.326 7.22e-15 1.08e-12 abundance 1530 959 1.44e-14 2.88e-13
Bacteroides_xylanisolvens diagnosis UC diagnosisUC -0.164 0.149 0.271 0.363 prevalence 1530 959 1.44e-14 2.88e-13
Clostridium_sp_AF20_17LB diagnosis UC diagnosisUC 2.15 0.262 9.44e-15 1.14e-12 abundance 1530 654 1.89e-14 3.69e-13
Clostridium_sp_AF20_17LB diagnosis UC diagnosisUC 0.71 0.147 1.33e-06 6.63e-06 prevalence 1530 654 1.89e-14 3.69e-13
Dysosmobacter_welbionis diagnosis UC diagnosisUC 1.33 0.161 1.01e-14 1.14e-12 abundance 1530 1190 2.02e-14 3.88e-13
Dysosmobacter_welbionis diagnosis UC diagnosisUC 0.478 0.192 0.0128 0.0266 prevalence 1530 1190 2.02e-14 3.88e-13
Bifidobacterium_adolescentis diagnosis CD diagnosisCD -0.685 0.346 0.0761 0.188 abundance 1530 427 2.25e-14 4.24e-13
Bifidobacterium_adolescentis diagnosis CD diagnosisCD -1.17 0.151 1.12e-14 2.48e-13 prevalence 1530 427 2.25e-14 4.24e-13
Clostridiales_bacterium reads reads reads -0.247 0.0796 1 1 abundance 1530 985 2.7e-14 5.01e-13
Clostridiales_bacterium reads reads reads 0.508 0.066 1.35e-14 2.91e-13 prevalence 1530 985 2.7e-14 5.01e-13
GGB1543_SGB2126 age age age -0.554 0.693 0.438 0.702 abundance 1530 42 2.81e-14 5.12e-13
GGB9713_SGB15249 diagnosis UC diagnosisUC -0.385 0.436 0.294 0.519 abundance 1530 329 3.15e-14 5.65e-13
GGB9713_SGB15249 diagnosis UC diagnosisUC -1.44 0.187 1.58e-14 3.27e-13 prevalence 1530 329 3.15e-14 5.65e-13
Clostridium_symbiosum diagnosis UC diagnosisUC -0.719 0.346 0.0227 0.0723 abundance 1530 539 4.2e-14 7.28e-13
Clostridium_symbiosum diagnosis UC diagnosisUC 1.25 0.163 2.1e-14 4.27e-13 prevalence 1530 539 4.2e-14 7.28e-13
Alistipes_onderdonkii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.01 0.675 3.95e-05 0.000404 abundance 1530 831 4.73e-14 8.06e-13
Alistipes_onderdonkii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.08 0.272 2.36e-14 4.71e-13 prevalence 1530 831 4.73e-14 8.06e-13
Odoribacter_splanchnicus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.07 0.395 0.0304 0.0902 abundance 1530 757 5.69e-14 9.55e-13
Odoribacter_splanchnicus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.96 0.257 2.85e-14 5.57e-13 prevalence 1530 757 5.69e-14 9.55e-13
Veillonella_parvula age age age 0.17 0.159 1 1 abundance 1530 547 1.04e-13 1.72e-12
Veillonella_parvula age age age -0.463 0.0615 5.2e-14 9.82e-13 prevalence 1530 547 1.04e-13 1.72e-12
Vescimonas_coprocola diagnosis UC diagnosisUC -0.0765 0.256 1 1 abundance 1530 599 1.11e-13 1.81e-12
Vescimonas_coprocola diagnosis UC diagnosisUC -1.12 0.149 5.55e-14 1.03e-12 prevalence 1530 599 1.11e-13 1.81e-12
Lachnospira_sp_NSJ_43 age age age 0.837 0.139 3.57e-09 1.46e-07 abundance 1530 296 1.17e-13 1.87e-12
Lachnospira_sp_NSJ_43 age age age 0.486 0.0646 5.83e-14 1.06e-12 prevalence 1530 296 1.17e-13 1.87e-12
Odoribacter_splanchnicus diagnosis UC diagnosisUC -0.72 0.187 2.58e-05 0.000283 abundance 1530 757 1.61e-13 2.55e-12
Odoribacter_splanchnicus diagnosis UC diagnosisUC -1.11 0.149 8.07e-14 1.45e-12 prevalence 1530 757 1.61e-13 2.55e-12
Blautia_wexlerae reads reads reads -0.497 0.0687 1 1 abundance 1530 1300 1.68e-13 2.62e-12
Blautia_wexlerae reads reads reads 0.657 0.0881 8.42e-14 1.48e-12 prevalence 1530 1300 1.68e-13 2.62e-12
Blautia_faecis reads reads reads -0.558 0.0751 1 1 abundance 1530 1120 1.73e-13 2.65e-12
Blautia_faecis reads reads reads 0.528 0.0708 8.64e-14 1.5e-12 prevalence 1530 1120 1.73e-13 2.65e-12
Roseburia_sp_AF02_12 diagnosis UC diagnosisUC 0.598 0.412 0.203 0.397 abundance 1530 363 2.39e-13 3.61e-12
Roseburia_sp_AF02_12 diagnosis UC diagnosisUC -1.22 0.165 1.2e-13 2.04e-12 prevalence 1530 363 2.39e-13 3.61e-12
Coprococcus_comes dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.42 0.684 0.00133 0.0076 abundance 1530 759 3.01e-13 4.49e-12
Coprococcus_comes dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.52 0.341 1.51e-13 2.53e-12 prevalence 1530 759 3.01e-13 4.49e-12
Firmicutes_bacterium_AF16_15 diagnosis CD diagnosisCD 0.0485 0.207 1 1 abundance 1530 827 3.38e-13 4.96e-12
Firmicutes_bacterium_AF16_15 diagnosis CD diagnosisCD -1.16 0.158 1.69e-13 2.79e-12 prevalence 1530 827 3.38e-13 4.96e-12
Dialister_invisus age age age 0.192 0.0944 1 1 abundance 1530 726 4.47e-13 6.48e-12
Dialister_invisus age age age -0.416 0.0567 2.24e-13 3.64e-12 prevalence 1530 726 4.47e-13 6.48e-12
Bilophila_wadsworthia dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.19 0.596 0.105 0.242 abundance 1530 764 4.72e-13 6.75e-12
Bilophila_wadsworthia dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.15 0.293 2.36e-13 3.78e-12 prevalence 1530 764 4.72e-13 6.75e-12
Faecalibacterium_SGB15346 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.39 0.848 0.000198 0.00151 abundance 1530 743 7.55e-13 1.06e-11
Faecalibacterium_SGB15346 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.47 0.341 3.78e-13 5.96e-12 prevalence 1530 743 7.55e-13 1.06e-11
Alistipes_shahii diagnosis UC diagnosisUC -0.547 0.21 0.00329 0.0154 abundance 1530 673 8.2e-13 1.14e-11
Alistipes_shahii diagnosis UC diagnosisUC -1.08 0.149 4.1e-13 6.38e-12 prevalence 1530 673 8.2e-13 1.14e-11
Bacteroides_eggerthii diagnosis CD diagnosisCD -1.86 0.573 0.00188 0.00989 abundance 1530 409 1.06e-12 1.45e-11
Bacteroides_eggerthii diagnosis CD diagnosisCD -1.09 0.152 5.28e-13 8.08e-12 prevalence 1530 409 1.06e-12 1.45e-11
Parabacteroides_distasonis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.576 0.667 0.142 0.302 abundance 1530 1140 1.09e-12 1.47e-11
Parabacteroides_distasonis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.88 0.4 5.43e-13 8.19e-12 prevalence 1530 1140 1.09e-12 1.47e-11
Clostridium_symbiosum age age age -0.478 0.146 0.00144 0.00812 abundance 1530 539 1.18e-12 1.58e-11
Clostridium_symbiosum age age age -0.459 0.0637 5.89e-13 8.78e-12 prevalence 1530 539 1.18e-12 1.58e-11
Alistipes_onderdonkii diagnosis UC diagnosisUC -1.05 0.265 2.27e-05 0.000255 abundance 1530 831 1.3e-12 1.71e-11
Alistipes_onderdonkii diagnosis UC diagnosisUC -1.09 0.152 6.49e-13 9.52e-12 prevalence 1530 831 1.3e-12 1.71e-11
Sutterella_wadsworthensis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.64 0.391 9.57e-13 8.61e-11 abundance 1530 536 1.91e-12 2.5e-11
Sutterella_wadsworthensis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.687 0.241 0.00433 0.00995 prevalence 1530 536 1.91e-12 2.5e-11
Blautia_wexlerae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.956 0.324 0.000296 0.00207 abundance 1530 1300 2.21e-12 2.85e-11
Blautia_wexlerae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.66 0.234 1.11e-12 1.6e-11 prevalence 1530 1300 2.21e-12 2.85e-11
Alistipes_communis age age age 0.321 0.105 0.00178 0.00942 abundance 1530 407 2.56e-12 3.26e-11
Alistipes_communis age age age 0.423 0.0596 1.28e-12 1.83e-11 prevalence 1530 407 2.56e-12 3.26e-11
Ruminococcus_lactaris diagnosis CD diagnosisCD -0.82 0.325 0.0214 0.0688 abundance 1530 379 3.48e-12 4.38e-11
Ruminococcus_lactaris diagnosis CD diagnosisCD -1.1 0.156 1.74e-12 2.46e-11 prevalence 1530 379 3.48e-12 4.38e-11
Parabacteroides_merdae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.56 0.51 5.11e-06 7.92e-05 abundance 1530 826 3.66e-12 4.55e-11
Parabacteroides_merdae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.87 0.266 1.83e-12 2.54e-11 prevalence 1530 826 3.66e-12 4.55e-11
GGB9713_SGB15249 age age age -0.15 0.138 1 1 abundance 1530 329 3.71e-12 4.57e-11
GGB9713_SGB15249 age age age 0.438 0.0622 1.86e-12 2.55e-11 prevalence 1530 329 3.71e-12 4.57e-11
Eubacterium_rectale antibiotics Yes antibioticsYes -0.368 0.273 0.28 0.501 abundance 1530 1210 5.32e-12 6.46e-11
Eubacterium_rectale antibiotics Yes antibioticsYes -1.41 0.201 2.66e-12 3.6e-11 prevalence 1530 1210 5.32e-12 6.46e-11
Blautia_obeum reads reads reads -0.342 0.089 1 1 abundance 1530 899 5.65e-12 6.79e-11
Blautia_obeum reads reads reads 0.417 0.0597 2.83e-12 3.78e-11 prevalence 1530 899 5.65e-12 6.79e-11
Clostridiaceae_bacterium dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.106 0.357 1 1 abundance 1530 1110 6.6e-12 7.84e-11
Clostridiaceae_bacterium dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.55 0.223 3.3e-12 4.36e-11 prevalence 1530 1110 6.6e-12 7.84e-11
Akkermansia_muciniphila age age age 0.292 0.141 0.0323 0.094 abundance 1530 407 7.32e-12 8.6e-11
Akkermansia_muciniphila age age age 0.403 0.058 3.66e-12 4.78e-11 prevalence 1530 407 7.32e-12 8.6e-11
Ruthenibacterium_lactatiformans reads reads reads -0.767 0.101 2.93e-05 0.000318 abundance 1530 797 7.86e-12 9.13e-11
Ruthenibacterium_lactatiformans reads reads reads 0.404 0.0582 3.93e-12 5.07e-11 prevalence 1530 797 7.86e-12 9.13e-11
Clostridium_sp_1001270H_150608_G6 diagnosis UC diagnosisUC -3.08 0.754 5.22e-05 0.000516 abundance 1530 141 9.16e-12 1.05e-10
Clostridium_sp_1001270H_150608_G6 diagnosis UC diagnosisUC -2.02 0.292 4.58e-12 5.83e-11 prevalence 1530 141 9.16e-12 1.05e-10
Firmicutes_bacterium_AF16_15 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.63 0.725 0.000922 0.00549 abundance 1530 827 1.4e-11 1.59e-10
Firmicutes_bacterium_AF16_15 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.12 0.309 6.99e-12 8.8e-11 prevalence 1530 827 1.4e-11 1.59e-10
Klebsiella_pneumoniae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 3.69 0.654 2.8e-08 8.99e-07 abundance 1530 119 1.43e-11 1.6e-10
Klebsiella_pneumoniae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.81 0.264 7.13e-12 8.87e-11 prevalence 1530 119 1.43e-11 1.6e-10
Bacteroides_stercoris dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.45 0.744 1.54e-05 0.000192 abundance 1530 826 1.66e-11 1.84e-10
Bacteroides_stercoris dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.82 0.266 8.28e-12 1.02e-10 prevalence 1530 826 1.66e-11 1.84e-10
Gemmiger_formicilis diagnosis CD diagnosisCD -0.469 0.252 0.113 0.256 abundance 1530 472 2.33e-11 2.57e-10
Gemmiger_formicilis diagnosis CD diagnosisCD -0.948 0.14 1.17e-11 1.42e-10 prevalence 1530 472 2.33e-11 2.57e-10
Eubacterium_rectale dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.23 0.708 0.243 0.451 abundance 1530 1210 2.53e-11 2.75e-10
Eubacterium_rectale dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.59 0.383 1.26e-11 1.52e-10 prevalence 1530 1210 2.53e-11 2.75e-10
Lacrimispora_celerecrescens diagnosis UC diagnosisUC 1.47 0.203 1.31e-11 9.92e-10 abundance 1530 756 2.61e-11 2.82e-10
Lacrimispora_celerecrescens diagnosis UC diagnosisUC 0.0908 0.146 0.535 0.629 prevalence 1530 756 2.61e-11 2.82e-10
Blautia_obeum diagnosis UC diagnosisUC 1.62 0.225 1.32e-11 9.92e-10 abundance 1530 899 2.64e-11 2.82e-10
Blautia_obeum diagnosis UC diagnosisUC 0.387 0.151 0.0106 0.0224 prevalence 1530 899 2.64e-11 2.82e-10
Clostridiaceae_bacterium reads reads reads -0.304 0.071 1 1 abundance 1530 1110 2.73e-11 2.88e-10
Clostridiaceae_bacterium reads reads reads 0.46 0.068 1.36e-11 1.62e-10 prevalence 1530 1110 2.73e-11 2.88e-10
Clostridium_sp_AF34_10BH reads reads reads -0.253 0.0925 1 1 abundance 1530 960 2.91e-11 3.05e-10
Clostridium_sp_AF34_10BH reads reads reads 0.433 0.0641 1.46e-11 1.71e-10 prevalence 1530 960 2.91e-11 3.05e-10
Oscillibacter_sp_ER4 age age age -0.0811 0.0963 1 1 abundance 1530 458 3.51e-11 3.64e-10
Oscillibacter_sp_ER4 age age age 0.385 0.0572 1.76e-11 2.04e-10 prevalence 1530 458 3.51e-11 3.64e-10
Dorea_longicatena dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.464 0.375 0.0695 0.176 abundance 1530 1020 3.6e-11 3.7e-10
Dorea_longicatena dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.51 0.224 1.8e-11 2.07e-10 prevalence 1530 1020 3.6e-11 3.7e-10
Ruminococcus_bicirculans diagnosis CD diagnosisCD 0.127 0.24 1 1 abundance 1530 678 8.04e-11 8.17e-10
Ruminococcus_bicirculans diagnosis CD diagnosisCD -0.903 0.137 4.02e-11 4.52e-10 prevalence 1530 678 8.04e-11 8.17e-10
Lachnospira_sp_NSJ_43 diagnosis UC diagnosisUC -0.786 0.383 0.0256 0.0798 abundance 1530 296 8.59e-11 8.65e-10
Lachnospira_sp_NSJ_43 diagnosis UC diagnosisUC -1.13 0.171 4.3e-11 4.78e-10 prevalence 1530 296 8.59e-11 8.65e-10
Enterocloster_bolteae diagnosis UC diagnosisUC -0.136 0.271 1 1 abundance 1530 866 1.03e-10 1.02e-09
Enterocloster_bolteae diagnosis UC diagnosisUC 0.975 0.149 5.13e-11 5.65e-10 prevalence 1530 866 1.03e-10 1.02e-09
Anaerostipes_hadrus antibiotics Yes antibioticsYes -0.209 0.29 1 1 abundance 1530 1130 1.04e-10 1.03e-09
Anaerostipes_hadrus antibiotics Yes antibioticsYes -1.28 0.194 5.2e-11 5.67e-10 prevalence 1530 1130 1.04e-10 1.03e-09
Alistipes_shahii diagnosis CD diagnosisCD -0.171 0.186 1 1 abundance 1530 673 1.1e-10 1.08e-09
Alistipes_shahii diagnosis CD diagnosisCD -0.898 0.137 5.52e-11 5.95e-10 prevalence 1530 673 1.1e-10 1.08e-09
Clostridium_sp_1001270H_150608_G6 diagnosis CD diagnosisCD 0.873 0.531 0.0784 0.191 abundance 1530 141 1.12e-10 1.09e-09
Clostridium_sp_1001270H_150608_G6 diagnosis CD diagnosisCD -1.42 0.216 5.6e-11 5.98e-10 prevalence 1530 141 1.12e-10 1.09e-09
Firmicutes_bacterium_AF16_15 age age age -0.435 0.0948 8.79e-06 0.000122 abundance 1530 827 1.2e-10 1.15e-09
Firmicutes_bacterium_AF16_15 age age age -0.395 0.0604 6e-11 6.34e-10 prevalence 1530 827 1.2e-10 1.15e-09
Roseburia_hominis diagnosis UC diagnosisUC 0.0713 0.231 1 1 abundance 1530 876 1.39e-10 1.33e-09
Roseburia_hominis diagnosis UC diagnosisUC -1.03 0.158 6.97e-11 7.29e-10 prevalence 1530 876 1.39e-10 1.33e-09
Flavonifractor_plautii age age age 0.0302 0.0736 1 1 abundance 1530 1220 1.42e-10 1.34e-09
Flavonifractor_plautii age age age -0.419 0.0642 7.08e-11 7.33e-10 prevalence 1530 1220 1.42e-10 1.34e-09
Alistipes_finegoldii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.73 0.85 0.00318 0.0152 abundance 1530 639 1.77e-10 1.66e-09
Alistipes_finegoldii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.29 0.354 8.87e-11 9.1e-10 prevalence 1530 639 1.77e-10 1.66e-09
Enterocloster_bolteae diagnosis CD diagnosisCD 0.635 0.253 0.00556 0.0236 abundance 1530 866 1.95e-10 1.81e-09
Enterocloster_bolteae diagnosis CD diagnosisCD 0.881 0.136 9.73e-11 9.89e-10 prevalence 1530 866 1.95e-10 1.81e-09
Collinsella_SGB14861 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.738 0.817 0.525 0.816 abundance 1530 593 2.07e-10 1.91e-09
Collinsella_SGB14861 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.29 0.354 1.04e-10 1.04e-09 prevalence 1530 593 2.07e-10 1.91e-09
Blautia_obeum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.573 0.5 0.114 0.256 abundance 1530 899 2.33e-10 2.13e-09
Blautia_obeum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.53 0.237 1.17e-10 1.16e-09 prevalence 1530 899 2.33e-10 2.13e-09
Alistipes_dispar age age age 0.834 0.269 0.00239 0.0121 abundance 1530 83 2.46e-10 2.21e-09
Alistipes_finegoldii diagnosis UC diagnosisUC -0.821 0.282 0.0016 0.00875 abundance 1530 639 2.48e-10 2.21e-09
Clostridium_fessum reads reads reads -0.381 0.0782 1 1 abundance 1530 926 2.48e-10 2.21e-09
Alistipes_dispar age age age 0.647 0.101 1.23e-10 1.2e-09 prevalence 1530 83 2.46e-10 2.21e-09
Alistipes_finegoldii diagnosis UC diagnosisUC -0.952 0.148 1.24e-10 1.2e-09 prevalence 1530 639 2.48e-10 2.21e-09
Clostridium_fessum reads reads reads 0.405 0.0629 1.24e-10 1.2e-09 prevalence 1530 926 2.48e-10 2.21e-09
Bacteroides_fragilis diagnosis CD diagnosisCD 1.75 0.28 1.52e-10 9.75e-09 abundance 1530 787 3.03e-10 2.67e-09
Bacteroides_fragilis diagnosis CD diagnosisCD 0.818 0.136 1.6e-09 1.24e-08 prevalence 1530 787 3.03e-10 2.67e-09
Ruminococcus_gnavus age age age -0.456 0.117 0.000161 0.0013 abundance 1530 767 3.17e-10 2.77e-09
Ruminococcus_gnavus age age age -0.356 0.0557 1.59e-10 1.52e-09 prevalence 1530 767 3.17e-10 2.77e-09
GGB33469_SGB15236 diagnosis UC diagnosisUC 0.603 0.417 0.204 0.398 abundance 1530 293 3.57e-10 3.09e-09
GGB33469_SGB15236 diagnosis UC diagnosisUC -1.18 0.186 1.78e-10 1.7e-09 prevalence 1530 293 3.57e-10 3.09e-09
GGB3175_SGB4191 diagnosis UC diagnosisUC 0.35 0.846 0.743 1 abundance 1530 154 4.27e-10 3.67e-09
GGB3175_SGB4191 diagnosis UC diagnosisUC -1.86 0.293 2.14e-10 2.02e-09 prevalence 1530 154 4.27e-10 3.67e-09
Roseburia_inulinivorans antibiotics Yes antibioticsYes -0.661 0.398 0.139 0.298 abundance 1530 951 4.41e-10 3.76e-09
Roseburia_inulinivorans antibiotics Yes antibioticsYes -1.26 0.199 2.2e-10 2.06e-09 prevalence 1530 951 4.41e-10 3.76e-09
Clostridium_symbiosum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.67 0.447 2.46e-10 1.48e-08 abundance 1530 539 4.92e-10 4.11e-09
GGB9453_SGB14844 age age age 0.132 0.175 1 1 abundance 1530 222 4.88e-10 4.11e-09
Lacrimispora_celerecrescens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.707 0.655 0.158 0.33 abundance 1530 756 4.94e-10 4.11e-09
Clostridium_symbiosum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.185 0.216 0.393 0.491 prevalence 1530 539 4.92e-10 4.11e-09
GGB9453_SGB14844 age age age 0.431 0.0681 2.44e-10 2.26e-09 prevalence 1530 222 4.88e-10 4.11e-09
Lacrimispora_celerecrescens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.07 0.327 2.47e-10 2.27e-09 prevalence 1530 756 4.94e-10 4.11e-09
Clostridium_sp_AM22_11AC reads reads reads -0.351 0.1 1 1 abundance 1530 730 7.24e-10 5.98e-09
Clostridium_sp_AM22_11AC reads reads reads 0.362 0.0577 3.62e-10 3.3e-09 prevalence 1530 730 7.24e-10 5.98e-09
Bilophila_wadsworthia reads reads reads -0.285 0.0852 1 1 abundance 1530 764 8.37e-10 6.86e-09
Bilophila_wadsworthia reads reads reads 0.374 0.0599 4.19e-10 3.78e-09 prevalence 1530 764 8.37e-10 6.86e-09
Dialister_invisus antibiotics Yes antibioticsYes -0.981 0.406 0.0255 0.0798 abundance 1530 726 8.73e-10 7.1e-09
Dialister_invisus antibiotics Yes antibioticsYes -1.3 0.208 4.37e-10 3.91e-09 prevalence 1530 726 8.73e-10 7.1e-09
Dysosmobacter_welbionis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.37 0.557 1 1 abundance 1530 1190 9e-10 7.27e-09
Dysosmobacter_welbionis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.35 0.378 4.5e-10 4e-09 prevalence 1530 1190 9e-10 7.27e-09
Ruminococcus_bromii diagnosis UC diagnosisUC -0.111 0.334 1 1 abundance 1530 429 9.24e-10 7.4e-09
Ruminococcus_bromii diagnosis UC diagnosisUC -1 0.161 4.62e-10 4.07e-09 prevalence 1530 429 9.24e-10 7.4e-09
Bacteroides_fragilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.79 0.478 4.87e-10 2.58e-08 abundance 1530 787 9.73e-10 7.74e-09
Bacteroides_fragilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.875 0.213 4.09e-05 0.000148 prevalence 1530 787 9.73e-10 7.74e-09
Clostridium_sp_AM22_11AC dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.3 0.698 0.123 0.272 abundance 1530 730 1.04e-09 8.24e-09
Clostridium_sp_AM22_11AC dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.91 0.307 5.22e-10 4.56e-09 prevalence 1530 730 1.04e-09 8.24e-09
Eubacterium_siraeum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.15 1.35 0.0309 0.0913 abundance 1530 565 1.19e-09 9.35e-09
Eubacterium_siraeum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.64 0.426 5.97e-10 5.17e-09 prevalence 1530 565 1.19e-09 9.35e-09
Bacteroides_thetaiotaomicron age age age 0.529 0.0902 2.93e-09 1.3e-07 abundance 1530 1060 1.44e-09 1.11e-08
Faecalibacterium_prausnitzii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.0662 0.36 0.349 0.588 abundance 1530 1370 1.43e-09 1.11e-08
Bacteroides_thetaiotaomicron age age age 0.423 0.0687 7.21e-10 6.15e-09 prevalence 1530 1060 1.44e-09 1.11e-08
Faecalibacterium_prausnitzii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.83 0.46 7.17e-10 6.15e-09 prevalence 1530 1370 1.43e-09 1.11e-08
Lacrimispora_amygdalina dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.86 0.491 2.49e-05 0.000277 abundance 1530 865 1.55e-09 1.19e-08
Lacrimispora_amygdalina dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.63 0.264 7.76e-10 6.56e-09 prevalence 1530 865 1.55e-09 1.19e-08
Phocaeicola_vulgatus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.22 0.746 0.000443 0.00293 abundance 1530 1290 1.6e-09 1.22e-08
Phocaeicola_vulgatus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.25 0.366 8.01e-10 6.72e-09 prevalence 1530 1290 1.6e-09 1.22e-08
Prevotella_copri_clade_A reads reads reads -0.427 0.254 1 1 abundance 1530 289 1.82e-09 1.38e-08
Prevotella_copri_clade_A reads reads reads 0.421 0.0687 9.11e-10 7.58e-09 prevalence 1530 289 1.82e-09 1.38e-08
Oscillospiraceae_bacterium age age age 0.227 0.264 0.37 0.617 abundance 1530 81 1.87e-09 1.4e-08
Oscillospiraceae_bacterium age age age 0.615 0.1 9.33e-10 7.71e-09 prevalence 1530 81 1.87e-09 1.4e-08
Alistipes_shahii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.21 0.693 1.8e-05 0.000211 abundance 1530 673 2.12e-09 1.58e-08
Alistipes_shahii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.16 0.355 1.06e-09 8.68e-09 prevalence 1530 673 2.12e-09 1.58e-08
Roseburia_hominis reads reads reads -0.421 0.098 1 1 abundance 1530 876 2.21e-09 1.63e-08
Roseburia_hominis reads reads reads 0.363 0.0595 1.11e-09 8.98e-09 prevalence 1530 876 2.21e-09 1.63e-08
Clostridium_fessum diagnosis UC diagnosisUC 0.0143 0.189 1 1 abundance 1530 926 2.51e-09 1.84e-08
Clostridium_fessum diagnosis UC diagnosisUC -0.968 0.159 1.25e-09 1.01e-08 prevalence 1530 926 2.51e-09 1.84e-08
Ruminococcus_torques reads reads reads -0.544 0.0767 1 1 abundance 1530 1090 2.54e-09 1.85e-08
Ruminococcus_torques reads reads reads 0.39 0.0643 1.27e-09 1.02e-08 prevalence 1530 1090 2.54e-09 1.85e-08
Clostridium_sp_AF20_17LB dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.727 1 0.347 0.587 abundance 1530 654 2.73e-09 1.98e-08
Clostridium_sp_AF20_17LB dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.55 0.421 1.37e-09 1.09e-08 prevalence 1530 654 2.73e-09 1.98e-08
GGB33469_SGB15236 age age age 0.366 0.152 0.0137 0.049 abundance 1530 293 2.92e-09 2.1e-08
GGB33469_SGB15236 age age age 0.382 0.0632 1.46e-09 1.15e-08 prevalence 1530 293 2.92e-09 2.1e-08
Coprococcus_eutactus diagnosis CD diagnosisCD -0.7 0.532 0.237 0.442 abundance 1530 177 3.01e-09 2.15e-08
Coprococcus_eutactus diagnosis CD diagnosisCD -1.35 0.224 1.5e-09 1.18e-08 prevalence 1530 177 3.01e-09 2.15e-08
Bacteroides_finegoldii diagnosis CD diagnosisCD -1.85 0.476 0.000218 0.00164 abundance 1530 333 3.29e-09 2.33e-08
Bacteroides_finegoldii diagnosis CD diagnosisCD -0.98 0.162 1.65e-09 1.27e-08 prevalence 1530 333 3.29e-09 2.33e-08
Faecalibacterium_SGB15315 reads reads reads -0.231 0.138 1 1 abundance 1530 619 4.57e-09 3.22e-08
Faecalibacterium_SGB15315 reads reads reads 0.355 0.0594 2.29e-09 1.75e-08 prevalence 1530 619 4.57e-09 3.22e-08
Bacteroides_ovatus age age age -0.47 0.0764 2.43e-09 1.22e-07 abundance 1530 1180 4.87e-09 3.41e-08
Bacteroides_ovatus age age age -0.196 0.0647 0.00246 0.006 prevalence 1530 1180 4.87e-09 3.41e-08
Firmicutes_bacterium_AF16_15 reads reads reads -0.251 0.0995 1 1 abundance 1530 827 4.99e-09 3.47e-08
Firmicutes_bacterium_AF16_15 reads reads reads 0.366 0.0614 2.49e-09 1.9e-08 prevalence 1530 827 4.99e-09 3.47e-08
Lachnospira_eligens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.491 0.515 0.168 0.346 abundance 1530 929 5.1e-09 3.52e-08
Lachnospira_eligens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.41 0.237 2.55e-09 1.92e-08 prevalence 1530 929 5.1e-09 3.52e-08
Sutterella_wadsworthensis age age age -0.621 0.101 2.85e-09 1.3e-07 abundance 1530 536 5.7e-09 3.92e-08
Sutterella_wadsworthensis age age age -0.271 0.0582 3.23e-06 1.5e-05 prevalence 1530 536 5.7e-09 3.92e-08
Clostridium_leptum reads reads reads -0.5 0.111 1 1 abundance 1530 652 5.78e-09 3.94e-08
Clostridium_leptum reads reads reads 0.348 0.0586 2.89e-09 2.17e-08 prevalence 1530 652 5.78e-09 3.94e-08
Bacteroides_ovatus diagnosis UC diagnosisUC 1.26 0.199 3.04e-09 1.3e-07 abundance 1530 1180 6.09e-09 4.12e-08
Bacteroides_ovatus diagnosis UC diagnosisUC 0.872 0.2 1.27e-05 5.22e-05 prevalence 1530 1180 6.09e-09 4.12e-08
Clostridium_sp_AF20_17LB reads reads reads -0.177 0.103 1 1 abundance 1530 654 6.36e-09 4.28e-08
Clostridium_sp_AF20_17LB reads reads reads 0.341 0.0575 3.18e-09 2.37e-08 prevalence 1530 654 6.36e-09 4.28e-08
Bacteroides_thetaiotaomicron reads reads reads -0.271 0.0982 1 1 abundance 1530 1060 6.77e-09 4.53e-08
Bacteroides_thetaiotaomicron reads reads reads 0.387 0.0655 3.38e-09 2.5e-08 prevalence 1530 1060 6.77e-09 4.53e-08
Roseburia_inulinivorans diagnosis CD diagnosisCD 0.148 0.198 1 1 abundance 1530 951 7.83e-09 5.21e-08
Roseburia_inulinivorans diagnosis CD diagnosisCD -0.883 0.15 3.92e-09 2.87e-08 prevalence 1530 951 7.83e-09 5.21e-08
Waltera_intestinalis diagnosis CD diagnosisCD -0.255 0.333 1 1 abundance 1530 524 7.99e-09 5.28e-08
Waltera_intestinalis diagnosis CD diagnosisCD -0.811 0.138 3.99e-09 2.91e-08 prevalence 1530 524 7.99e-09 5.28e-08
Alistipes_communis diagnosis UC diagnosisUC -1.04 0.337 0.000997 0.00586 abundance 1530 407 8.62e-09 5.66e-08
Alistipes_communis diagnosis UC diagnosisUC -1.03 0.176 4.31e-09 3.12e-08 prevalence 1530 407 8.62e-09 5.66e-08
Dysosmobacter_sp_BX15 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.83 0.724 8.06e-07 1.69e-05 abundance 1530 621 8.99e-09 5.86e-08
Dysosmobacter_sp_BX15 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.19 0.373 4.49e-09 3.23e-08 prevalence 1530 621 8.99e-09 5.86e-08
Clostridium_sp_AT4 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 3.32 0.594 4.85e-09 1.9e-07 abundance 1530 528 9.7e-09 6.29e-08
Clostridium_sp_AT4 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.06 0.273 0.000108 0.000353 prevalence 1530 528 9.7e-09 6.29e-08
Clostridium_sp_AT4 reads reads reads -0.533 0.101 1 1 abundance 1530 528 1e-08 6.48e-08
Clostridium_sp_AT4 reads reads reads 0.342 0.0586 5.02e-09 3.59e-08 prevalence 1530 528 1e-08 6.48e-08
Coprococcus_comes diagnosis UC diagnosisUC 1.29 0.206 5.26e-09 1.97e-07 abundance 1530 759 1.05e-08 6.74e-08
Coprococcus_comes diagnosis UC diagnosisUC -0.13 0.144 0.367 0.465 prevalence 1530 759 1.05e-08 6.74e-08
GGB33512_SGB15201 age age age 0.483 0.0844 1.08e-08 7.48e-08 prevalence 1530 121 1.08e-08 6.9e-08
Anaerostipes_hadrus age age age -0.359 0.0706 9.16e-07 1.87e-05 abundance 1530 1130 1.15e-08 7.29e-08
Anaerostipes_hadrus age age age -0.363 0.0624 5.76e-09 4.09e-08 prevalence 1530 1130 1.15e-08 7.29e-08
Eubacterium_ventriosum diagnosis CD diagnosisCD -0.0287 0.273 1 1 abundance 1530 520 1.24e-08 7.79e-08
Eubacterium_ventriosum diagnosis CD diagnosisCD -0.802 0.138 6.19e-09 4.36e-08 prevalence 1530 520 1.24e-08 7.79e-08
Eubacterium_siraeum age age age 0.142 0.127 1 1 abundance 1530 565 1.26e-08 7.88e-08
Eubacterium_siraeum age age age 0.326 0.0561 6.3e-09 4.41e-08 prevalence 1530 565 1.26e-08 7.88e-08
Enterocloster_clostridioformis age age age 0.914 0.155 7.04e-09 2.53e-07 abundance 1530 312 1.41e-08 8.75e-08
Enterocloster_clostridioformis age age age 0.345 0.063 4.47e-08 2.76e-07 prevalence 1530 312 1.41e-08 8.75e-08
Fusicatenibacter_saccharivorans antibiotics Yes antibioticsYes -0.154 0.269 1 1 abundance 1530 1120 1.51e-08 9.36e-08
Fusicatenibacter_saccharivorans antibiotics Yes antibioticsYes -1.16 0.2 7.57e-09 5.27e-08 prevalence 1530 1120 1.51e-08 9.36e-08
Lachnospira_eligens reads reads reads -0.57 0.0896 1 1 abundance 1530 929 2.47e-08 1.51e-07
Oscillospiraceae_bacterium diagnosis UC diagnosisUC -4.05 0.643 1.23e-08 4.26e-07 abundance 1530 81 2.46e-08 1.51e-07
Lachnospira_eligens reads reads reads 0.342 0.06 1.24e-08 8.49e-08 prevalence 1530 929 2.47e-08 1.51e-07
Oscillospiraceae_bacterium diagnosis UC diagnosisUC -0.615 0.262 0.019 0.0373 prevalence 1530 81 2.46e-08 1.51e-07
Clostridium_leptum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.12 1.14 1 1 abundance 1530 652 2.73e-08 1.65e-07
Clostridium_sp_AF36_4 diagnosis CD diagnosisCD 0.369 0.211 0.0389 0.109 abundance 1530 568 2.72e-08 1.65e-07
Clostridium_leptum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.59 0.457 1.36e-08 9.24e-08 prevalence 1530 652 2.73e-08 1.65e-07
Clostridium_sp_AF36_4 diagnosis CD diagnosisCD -0.776 0.137 1.36e-08 9.24e-08 prevalence 1530 568 2.72e-08 1.65e-07
Collinsella_aerofaciens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.224 0.572 0.439 0.702 abundance 1530 698 3.09e-08 1.85e-07
Collinsella_aerofaciens dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.5 0.266 1.54e-08 1.04e-07 prevalence 1530 698 3.09e-08 1.85e-07
Collinsella_SGB14861 diagnosis UC diagnosisUC 0.386 0.284 0.27 0.485 abundance 1530 593 3.7e-08 2.21e-07
Collinsella_SGB14861 diagnosis UC diagnosisUC -0.843 0.15 1.85e-08 1.24e-07 prevalence 1530 593 3.7e-08 2.21e-07
Flavonifractor_plautii diagnosis CD diagnosisCD 0.919 0.175 1.94e-08 6.48e-07 abundance 1530 1220 3.89e-08 2.31e-07
Flavonifractor_plautii diagnosis CD diagnosisCD 0.692 0.177 8.97e-05 0.000297 prevalence 1530 1220 3.89e-08 2.31e-07
GGB9708_SGB15234 age age age 0.338 0.16 0.03 0.0895 abundance 1530 282 4.02e-08 2.37e-07
GGB9708_SGB15234 age age age 0.358 0.0637 2.01e-08 1.34e-07 prevalence 1530 282 4.02e-08 2.37e-07
Bacteroides_uniformis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.694 0.561 0.0508 0.136 abundance 1530 1240 4.33e-08 2.54e-07
Bacteroides_uniformis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.98 0.353 2.17e-08 1.43e-07 prevalence 1530 1240 4.33e-08 2.54e-07
Oscillibacter_sp_ER4 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.89 0.878 0.00247 0.0123 abundance 1530 458 5.2e-08 3.04e-07
Oscillibacter_sp_ER4 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.37 0.427 2.6e-08 1.71e-07 prevalence 1530 458 5.2e-08 3.04e-07
Bacteroides_uniformis reads reads reads -0.0532 0.069 3.01e-05 0.000323 abundance 1530 1240 5.32e-08 3.09e-07
Bacteroides_uniformis reads reads reads 0.447 0.0803 2.66e-08 1.73e-07 prevalence 1530 1240 5.32e-08 3.09e-07
Eubacterium_siraeum diagnosis UC diagnosisUC -1.08 0.375 0.00222 0.0113 abundance 1530 565 5.42e-08 3.13e-07
Eubacterium_siraeum diagnosis UC diagnosisUC -0.838 0.151 2.71e-08 1.76e-07 prevalence 1530 565 5.42e-08 3.13e-07
Ruthenibacterium_lactatiformans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.879 0.531 0.0392 0.11 abundance 1530 797 5.49e-08 3.16e-07
Ruthenibacterium_lactatiformans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.33 0.24 2.75e-08 1.77e-07 prevalence 1530 797 5.49e-08 3.16e-07
Bilophila_wadsworthia diagnosis UC diagnosisUC 0.457 0.226 0.0894 0.213 abundance 1530 764 5.59e-08 3.19e-07
Bilophila_wadsworthia diagnosis UC diagnosisUC -0.828 0.149 2.79e-08 1.79e-07 prevalence 1530 764 5.59e-08 3.19e-07
Enterocloster_bolteae reads reads reads -0.494 0.0968 1 1 abundance 1530 866 5.96e-08 3.39e-07
Enterocloster_bolteae reads reads reads 0.313 0.0565 2.98e-08 1.9e-07 prevalence 1530 866 5.96e-08 3.39e-07
Parasutterella_excrementihominis diagnosis CD diagnosisCD 1.21 0.249 3.53e-07 8.14e-06 abundance 1530 699 6.19e-08 3.5e-07
Parasutterella_excrementihominis diagnosis CD diagnosisCD -0.749 0.135 3.09e-08 1.96e-07 prevalence 1530 699 6.19e-08 3.5e-07
Enterocloster_bolteae age age age 0.515 0.0942 3.14e-08 9.76e-07 abundance 1530 866 6.29e-08 3.53e-07
Enterocloster_bolteae age age age -0.0852 0.0538 0.113 0.175 prevalence 1530 866 6.29e-08 3.53e-07
Proteus_mirabilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 3.55 0.985 0.000236 0.00174 abundance 1530 100 6.4e-08 3.58e-07
Proteus_mirabilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.81 0.327 3.2e-08 2.01e-07 prevalence 1530 100 6.4e-08 3.58e-07
GGB3746_SGB5089 antibiotics Yes antibioticsYes -0.454 0.528 0.47 0.741 abundance 1530 651 6.75e-08 3.75e-07
GGB3746_SGB5089 antibiotics Yes antibioticsYes -1.28 0.232 3.37e-08 2.11e-07 prevalence 1530 651 6.75e-08 3.75e-07
Parasutterella_SGB9260 diagnosis UC diagnosisUC 1.7 0.357 7.72e-06 0.000109 abundance 1530 269 7.06e-08 3.91e-07
Parasutterella_SGB9260 diagnosis UC diagnosisUC 1.01 0.183 3.53e-08 2.2e-07 prevalence 1530 269 7.06e-08 3.91e-07
Anaerostipes_hadrus diagnosis UC diagnosisUC 1.07 0.181 4.01e-08 1.2e-06 abundance 1530 1130 8.02e-08 4.41e-07
Anaerostipes_hadrus diagnosis UC diagnosisUC -0.367 0.184 0.0463 0.0813 prevalence 1530 1130 8.02e-08 4.41e-07
Clostridium_sp_AF34_10BH diagnosis UC diagnosisUC -0.476 0.226 0.0157 0.0543 abundance 1530 960 9.62e-08 5.27e-07
Clostridium_sp_AF34_10BH diagnosis UC diagnosisUC -0.92 0.169 4.81e-08 2.95e-07 prevalence 1530 960 9.62e-08 5.27e-07
Akkermansia_sp_KLE1798 diagnosis CD diagnosisCD -1.52 0.285 9.85e-08 5.82e-07 prevalence 1530 70 9.85e-08 5.37e-07
Clostridium_sp_AF36_4 diagnosis UC diagnosisUC 0.107 0.231 1 1 abundance 1530 568 1.26e-07 6.81e-07
Clostridium_sp_AF36_4 diagnosis UC diagnosisUC -0.802 0.148 6.29e-08 3.82e-07 prevalence 1530 568 1.26e-07 6.81e-07
Roseburia_hominis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.44 0.524 0.00161 0.00875 abundance 1530 876 1.38e-07 7.46e-07
Roseburia_hominis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.27 0.236 6.91e-08 4.18e-07 prevalence 1530 876 1.38e-07 7.46e-07
Faecalibacterium_SGB15315 diagnosis CD diagnosisCD 1 0.3 0.000394 0.00267 abundance 1530 619 1.42e-07 7.64e-07
Faecalibacterium_SGB15315 diagnosis CD diagnosisCD -0.74 0.137 7.12e-08 4.28e-07 prevalence 1530 619 1.42e-07 7.64e-07
Roseburia_faecis age age age -0.125 0.0887 1 1 abundance 1530 922 1.52e-07 8.12e-07
Roseburia_faecis age age age 0.314 0.0585 7.61e-08 4.54e-07 prevalence 1530 922 1.52e-07 8.12e-07
Clostridium_sp_AT4 diagnosis CD diagnosisCD 0.3 0.311 0.235 0.44 abundance 1530 528 1.57e-07 8.31e-07
Clostridium_sp_AT4 diagnosis CD diagnosisCD 0.814 0.152 7.83e-08 4.65e-07 prevalence 1530 528 1.57e-07 8.31e-07
Fusicatenibacter_saccharivorans reads reads reads -0.451 0.0701 1 1 abundance 1530 1120 2.07e-07 1.09e-06
Fusicatenibacter_saccharivorans reads reads reads 0.367 0.0689 1.04e-07 6.08e-07 prevalence 1530 1120 2.07e-07 1.09e-06
Lactobacillus_acidophilus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.35 0.453 2.16e-07 1.19e-06 prevalence 1530 26 2.16e-07 1.13e-06
Dysosmobacter_welbionis diagnosis CD diagnosisCD 0.726 0.149 1.11e-07 3.11e-06 abundance 1530 1190 2.21e-07 1.16e-06
Dysosmobacter_welbionis diagnosis CD diagnosisCD 0.492 0.179 0.00607 0.0135 prevalence 1530 1190 2.21e-07 1.16e-06
Lacrimispora_amygdalina reads reads reads -0.318 0.077 1 1 abundance 1530 865 2.23e-07 1.16e-06
Lacrimispora_amygdalina reads reads reads 0.313 0.0591 1.12e-07 6.52e-07 prevalence 1530 865 2.23e-07 1.16e-06
Alistipes_communis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.06 0.805 0.295 0.52 abundance 1530 407 2.34e-07 1.21e-06
Alistipes_communis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2 0.378 1.17e-07 6.79e-07 prevalence 1530 407 2.34e-07 1.21e-06
Eubacterium_rectale age age age -0.357 0.065 1.21e-07 3.3e-06 abundance 1530 1210 2.42e-07 1.25e-06
Eubacterium_rectale age age age 0.199 0.0773 0.00995 0.021 prevalence 1530 1210 2.42e-07 1.25e-06
GGB3746_SGB5089 reads reads reads -0.538 0.109 1 1 abundance 1530 651 2.65e-07 1.36e-06
GGB3746_SGB5089 reads reads reads 0.304 0.0575 1.33e-07 7.66e-07 prevalence 1530 651 2.65e-07 1.36e-06
Roseburia_hominis diagnosis CD diagnosisCD -0.339 0.206 0.189 0.377 abundance 1530 876 2.72e-07 1.39e-06
Roseburia_hominis diagnosis CD diagnosisCD -0.78 0.148 1.36e-07 7.82e-07 prevalence 1530 876 2.72e-07 1.39e-06
Roseburia_inulinivorans reads reads reads -0.114 0.0856 1 1 abundance 1530 951 2.93e-07 1.49e-06
Roseburia_inulinivorans reads reads reads 0.32 0.0609 1.47e-07 8.38e-07 prevalence 1530 951 2.93e-07 1.49e-06
Bacteroides_stercoris dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.494 1.3 0.489 0.766 abundance 1530 826 2.98e-07 1.51e-06
Bacteroides_stercoris dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.37 0.451 1.49e-07 8.46e-07 prevalence 1530 826 2.98e-07 1.51e-06
Clostridium_sp_AF34_10BH antibiotics Yes antibioticsYes -0.437 0.381 0.339 0.58 abundance 1530 960 3e-07 1.51e-06
Clostridium_sp_AF34_10BH antibiotics Yes antibioticsYes -1.05 0.199 1.5e-07 8.48e-07 prevalence 1530 960 3e-07 1.51e-06
Collinsella_aerofaciens diagnosis UC diagnosisUC 1.36 0.242 1.54e-07 4.08e-06 abundance 1530 698 3.08e-07 1.54e-06
Collinsella_aerofaciens diagnosis UC diagnosisUC 0.132 0.143 0.357 0.455 prevalence 1530 698 3.08e-07 1.54e-06
Oscillospiraceae_bacterium diagnosis CD diagnosisCD -3.76 1.05 0.000761 0.00466 abundance 1530 81 3.33e-07 1.66e-06
Oscillospiraceae_bacterium diagnosis CD diagnosisCD -2.05 0.392 1.66e-07 9.36e-07 prevalence 1530 81 3.33e-07 1.66e-06
Bacteroides_salyersiae age age age 1.16 0.212 1.78e-07 4.59e-06 abundance 1530 150 3.57e-07 1.77e-06
Bacteroides_salyersiae age age age 0.38 0.0805 2.41e-06 1.17e-05 prevalence 1530 150 3.57e-07 1.77e-06
Faecalibacterium_SGB15315 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.42 1.53 0.149 0.315 abundance 1530 619 3.73e-07 1.84e-06
Faecalibacterium_SGB15315 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.62 0.503 1.87e-07 1.04e-06 prevalence 1530 619 3.73e-07 1.84e-06
Fusicatenibacter_saccharivorans diagnosis UC diagnosisUC 0.676 0.178 0.000719 0.00446 abundance 1530 1120 4.01e-07 1.97e-06
Fusicatenibacter_saccharivorans diagnosis UC diagnosisUC -0.969 0.186 2e-07 1.11e-06 prevalence 1530 1120 4.01e-07 1.97e-06
Ruminococcus_bromii age age age 0.0414 0.115 1 1 abundance 1530 429 4.83e-07 2.36e-06
Ruminococcus_bromii age age age 0.298 0.0577 2.41e-07 1.33e-06 prevalence 1530 429 4.83e-07 2.36e-06
Parabacteroides_merdae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.28 0.976 0.00608 0.0256 abundance 1530 826 4.88e-07 2.38e-06
Parabacteroides_merdae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.5 0.485 2.44e-07 1.34e-06 prevalence 1530 826 4.88e-07 2.38e-06
Parasutterella_SGB9260 diagnosis CD diagnosisCD 1.94 0.38 2.48e-07 6.19e-06 abundance 1530 269 4.95e-07 2.4e-06
Parasutterella_SGB9260 diagnosis CD diagnosisCD 0.191 0.186 0.306 0.402 prevalence 1530 269 4.95e-07 2.4e-06
GGB6601_SGB9333 age age age 0.533 0.107 5.67e-07 2.98e-06 prevalence 1530 69 5.67e-07 2.74e-06
Lacrimispora_celerecrescens age age age -0.36 0.0867 6.32e-05 0.000599 abundance 1530 756 6.19e-07 2.97e-06
Lacrimispora_celerecrescens age age age -0.284 0.0554 3.09e-07 1.69e-06 prevalence 1530 756 6.19e-07 2.97e-06
Ruminococcus_torques diagnosis CD diagnosisCD 0.879 0.184 3.25e-07 7.74e-06 abundance 1530 1090 6.49e-07 3.11e-06
Ruminococcus_torques diagnosis CD diagnosisCD -0.696 0.164 2.15e-05 8.32e-05 prevalence 1530 1090 6.49e-07 3.11e-06
Parabacteroides_distasonis reads reads reads -0.032 0.0603 3.27e-07 7.74e-06 abundance 1530 1140 6.54e-07 3.11e-06
Parabacteroides_distasonis reads reads reads 0.211 0.0671 0.00166 0.00425 prevalence 1530 1140 6.54e-07 3.11e-06
Akkermansia_muciniphila diagnosis UC diagnosisUC -0.356 0.456 0.349 0.588 abundance 1530 407 7.71e-07 3.64e-06
GGB9708_SGB15234 diagnosis UC diagnosisUC 0.652 0.488 0.236 0.441 abundance 1530 282 7.71e-07 3.64e-06
Akkermansia_muciniphila diagnosis UC diagnosisUC -0.842 0.166 3.85e-07 2.08e-06 prevalence 1530 407 7.71e-07 3.64e-06
GGB9708_SGB15234 diagnosis UC diagnosisUC -0.96 0.189 3.85e-07 2.08e-06 prevalence 1530 282 7.71e-07 3.64e-06
Dorea_longicatena diagnosis UC diagnosisUC 1.01 0.184 3.91e-07 8.8e-06 abundance 1530 1020 7.83e-07 3.68e-06
Dorea_longicatena diagnosis UC diagnosisUC -0.123 0.16 0.443 0.546 prevalence 1530 1020 7.83e-07 3.68e-06
Prevotella_copri_clade_A age age age -0.551 0.348 0.122 0.272 abundance 1530 289 8.08e-07 3.78e-06
Prevotella_copri_clade_A age age age -0.387 0.0763 4.04e-07 2.17e-06 prevalence 1530 289 8.08e-07 3.78e-06
Faecalibacterium_SGB15346 reads reads reads -0.678 0.0997 0.000798 0.00485 abundance 1530 743 9.04e-07 4.21e-06
Faecalibacterium_SGB15346 reads reads reads 0.287 0.057 4.52e-07 2.41e-06 prevalence 1530 743 9.04e-07 4.21e-06
Bacteroides_xylanisolvens reads reads reads -0.56 0.118 1 1 abundance 1530 959 9.5e-07 4.41e-06
Bacteroides_xylanisolvens reads reads reads 0.302 0.0599 4.75e-07 2.52e-06 prevalence 1530 959 9.5e-07 4.41e-06
Candidatus_Cibionibacter_quicibialis reads reads reads -0.348 0.0873 1 1 abundance 1530 933 1.02e-06 4.7e-06
Candidatus_Cibionibacter_quicibialis reads reads reads 0.299 0.0596 5.09e-07 2.69e-06 prevalence 1530 933 1.02e-06 4.7e-06
Oscillibacter_sp_ER4 diagnosis UC diagnosisUC 0.131 0.267 1 1 abundance 1530 458 1.23e-06 5.67e-06
Oscillibacter_sp_ER4 diagnosis UC diagnosisUC -0.789 0.158 6.17e-07 3.23e-06 prevalence 1530 458 1.23e-06 5.67e-06
Bacteroides_stercoris age age age -0.602 0.118 6.64e-07 1.46e-05 abundance 1530 826 1.33e-06 6.06e-06
Blautia_wexlerae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.546 0.508 1 1 abundance 1530 1300 1.33e-06 6.06e-06
Bacteroides_stercoris age age age -0.0954 0.054 0.0772 0.125 prevalence 1530 826 1.33e-06 6.06e-06
Blautia_wexlerae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.86 0.373 6.65e-07 3.46e-06 prevalence 1530 1300 1.33e-06 6.06e-06
Roseburia_inulinivorans dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.309 0.754 0.345 0.586 abundance 1530 951 1.37e-06 6.23e-06
Roseburia_inulinivorans dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.87 0.377 6.87e-07 3.56e-06 prevalence 1530 951 1.37e-06 6.23e-06
Phocaeicola_plebeius diagnosis CD diagnosisCD -3.91 0.732 6.98e-07 1.49e-05 abundance 1530 127 1.4e-06 6.3e-06
Phocaeicola_plebeius diagnosis CD diagnosisCD 0.3 0.271 0.269 0.36 prevalence 1530 127 1.4e-06 6.3e-06
Clostridium_sp_AF36_4 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.465 0.723 1 1 abundance 1530 568 1.63e-06 7.34e-06
Clostridium_sp_AF36_4 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.76 0.358 8.16e-07 4.21e-06 prevalence 1530 568 1.63e-06 7.34e-06
Eisenbergiella_massiliensis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.47 0.947 0.0048 0.021 abundance 1530 417 1.89e-06 8.45e-06
GGB33469_SGB15236 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -6.45 1.24 9.48e-07 1.88e-05 abundance 1530 293 1.9e-06 8.45e-06
Eisenbergiella_massiliensis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.61 0.329 9.47e-07 4.86e-06 prevalence 1530 417 1.89e-06 8.45e-06
GGB33469_SGB15236 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.97 0.51 0.000108 0.000353 prevalence 1530 293 1.9e-06 8.45e-06
Phascolarctobacterium_succinatutens diagnosis CD diagnosisCD -0.728 0.387 0.0914 0.216 abundance 1530 125 1.91e-06 8.46e-06
Phascolarctobacterium_succinatutens diagnosis CD diagnosisCD -1.25 0.256 9.53e-07 4.87e-06 prevalence 1530 125 1.91e-06 8.46e-06
Bacteroides_cellulosilyticus diagnosis UC diagnosisUC -1.76 0.369 9.59e-07 1.88e-05 abundance 1530 433 1.92e-06 8.49e-06
Bacteroides_cellulosilyticus diagnosis UC diagnosisUC -0.344 0.158 0.0289 0.0542 prevalence 1530 433 1.92e-06 8.49e-06
Gemmiger_formicilis antibiotics Yes antibioticsYes 0.386 0.356 0.199 0.392 abundance 1530 472 1.94e-06 8.54e-06
Gemmiger_formicilis antibiotics Yes antibioticsYes 0.938 0.191 9.7e-07 4.93e-06 prevalence 1530 472 1.94e-06 8.54e-06
Ruminococcus_torques dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.213 0.686 1 1 abundance 1530 1090 2.16e-06 9.49e-06
Ruminococcus_torques dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.74 0.357 1.08e-06 5.47e-06 prevalence 1530 1090 2.16e-06 9.49e-06
Blautia_faecis diagnosis UC diagnosisUC 0.985 0.186 1.11e-06 2.13e-05 abundance 1530 1120 2.22e-06 9.71e-06
Blautia_faecis diagnosis UC diagnosisUC 0.336 0.179 0.0602 0.101 prevalence 1530 1120 2.22e-06 9.71e-06
Blautia_wexlerae age age age -0.122 0.0687 1 1 abundance 1530 1300 2.27e-06 9.87e-06
Blautia_wexlerae age age age -0.367 0.0755 1.13e-06 5.71e-06 prevalence 1530 1300 2.27e-06 9.87e-06
Dorea_longicatena antibiotics Yes antibioticsYes -0.0691 0.274 1 1 abundance 1530 1020 2.4e-06 1.04e-05
Dorea_longicatena antibiotics Yes antibioticsYes -0.902 0.186 1.2e-06 6.02e-06 prevalence 1530 1020 2.4e-06 1.04e-05
Akkermansia_sp_KLE1798 diagnosis UC diagnosisUC -2.86 0.609 2.62e-06 1.26e-05 prevalence 1530 70 2.62e-06 1.13e-05
Blautia_obeum diagnosis CD diagnosisCD 0.954 0.21 1.37e-06 2.58e-05 abundance 1530 899 2.75e-06 1.18e-05
Blautia_obeum diagnosis CD diagnosisCD 0.105 0.137 0.445 0.548 prevalence 1530 899 2.75e-06 1.18e-05
Bifidobacterium_longum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.462 0.819 1 1 abundance 1530 843 2.81e-06 1.2e-05
Phocaeicola_dorei age age age 0.524 0.189 0.00485 0.021 abundance 1530 769 2.81e-06 1.2e-05
Bifidobacterium_longum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.8 0.374 1.41e-06 6.95e-06 prevalence 1530 843 2.81e-06 1.2e-05
Phocaeicola_dorei age age age 0.27 0.0561 1.4e-06 6.95e-06 prevalence 1530 769 2.81e-06 1.2e-05
Bacteroides_caccae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.543 0.776 1 1 abundance 1530 958 3.03e-06 1.29e-05
Bacteroides_caccae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.95 0.406 1.52e-06 7.45e-06 prevalence 1530 958 3.03e-06 1.29e-05
Lacrimispora_amygdalina diagnosis UC diagnosisUC 0.987 0.189 1.64e-06 3.02e-05 abundance 1530 865 3.28e-06 1.39e-05
Lacrimispora_amygdalina diagnosis UC diagnosisUC -0.0931 0.155 0.548 0.64 prevalence 1530 865 3.28e-06 1.39e-05
Bacteroides_finegoldii antibiotics Yes antibioticsYes 2.7 0.571 1.92e-06 3.45e-05 abundance 1530 333 3.83e-06 1.61e-05
Bacteroides_finegoldii antibiotics Yes antibioticsYes 0.926 0.212 1.26e-05 5.2e-05 prevalence 1530 333 3.83e-06 1.61e-05
Clostridium_sp_AF34_10BH diagnosis CD diagnosisCD -0.596 0.208 0.0114 0.042 abundance 1530 960 3.86e-06 1.62e-05
Clostridium_sp_AF34_10BH diagnosis CD diagnosisCD -0.758 0.159 1.93e-06 9.44e-06 prevalence 1530 960 3.86e-06 1.62e-05
Clostridiaceae_bacterium diagnosis UC diagnosisUC 0.456 0.175 0.0286 0.0857 abundance 1530 1110 4.16e-06 1.74e-05
Clostridiaceae_bacterium diagnosis UC diagnosisUC -0.893 0.188 2.08e-06 1.01e-05 prevalence 1530 1110 4.16e-06 1.74e-05
Phocaeicola_plebeius diagnosis UC diagnosisUC -3.67 0.751 2.19e-06 3.87e-05 abundance 1530 127 4.39e-06 1.83e-05
Phocaeicola_plebeius diagnosis UC diagnosisUC 1.01 0.257 8.8e-05 0.000292 prevalence 1530 127 4.39e-06 1.83e-05
Escherichia_coli antibiotics Yes antibioticsYes 2.02 0.439 2.33e-06 4.03e-05 abundance 1530 707 4.65e-06 1.93e-05
Escherichia_coli antibiotics Yes antibioticsYes -0.746 0.193 0.000111 0.00036 prevalence 1530 707 4.65e-06 1.93e-05
Flavonifractor_plautii diagnosis UC diagnosisUC 0.973 0.19 2.43e-06 4.12e-05 abundance 1530 1220 4.86e-06 2.01e-05
Flavonifractor_plautii diagnosis UC diagnosisUC 0.752 0.189 6.76e-05 0.000231 prevalence 1530 1220 4.86e-06 2.01e-05
Barnesiella_intestinihominis diagnosis UC diagnosisUC -1.17 0.317 0.000104 0.000887 abundance 1530 431 5.04e-06 2.07e-05
Barnesiella_intestinihominis diagnosis UC diagnosisUC -0.736 0.156 2.52e-06 1.22e-05 prevalence 1530 431 5.04e-06 2.07e-05
Eubacterium_ventriosum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.12 1.26 0.133 0.29 abundance 1530 520 5.25e-06 2.15e-05
Eubacterium_ventriosum dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.36 0.503 2.63e-06 1.26e-05 prevalence 1530 520 5.25e-06 2.15e-05
Clostridium_leptum diagnosis CD diagnosisCD -0.89 0.24 0.000659 0.00412 abundance 1530 652 5.48e-06 2.24e-05
Clostridium_leptum diagnosis CD diagnosisCD -0.635 0.135 2.74e-06 1.3e-05 prevalence 1530 652 5.48e-06 2.24e-05
Phocaeicola_coprocola diagnosis UC diagnosisUC 5.27 2.45 0.0367 0.105 abundance 1530 101 5.59e-06 2.27e-05
Phocaeicola_coprocola diagnosis UC diagnosisUC 2.86 0.61 2.79e-06 1.32e-05 prevalence 1530 101 5.59e-06 2.27e-05
Bacteroides_cellulosilyticus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.78 1.02 0.0122 0.0446 abundance 1530 433 5.61e-06 2.27e-05
Bacteroides_cellulosilyticus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.7 0.363 2.81e-06 1.32e-05 prevalence 1530 433 5.61e-06 2.27e-05
Lachnospira_eligens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.965 0.763 0.462 0.731 abundance 1530 929 5.67e-06 2.29e-05
Lachnospira_eligens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.71 0.365 2.84e-06 1.33e-05 prevalence 1530 929 5.67e-06 2.29e-05
Clostridiaceae_bacterium dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.11 0.639 0.646 0.967 abundance 1530 1110 5.72e-06 2.3e-05
Clostridiaceae_bacterium dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.74 0.372 2.86e-06 1.34e-05 prevalence 1530 1110 5.72e-06 2.3e-05
GGB3278_SGB4328 diagnosis CD diagnosisCD -0.827 0.493 0.126 0.278 abundance 1530 179 6.32e-06 2.53e-05
GGB3278_SGB4328 diagnosis CD diagnosisCD -0.905 0.194 3.16e-06 1.47e-05 prevalence 1530 179 6.32e-06 2.53e-05
Flavonifractor_plautii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.2 0.303 3.27e-06 5.35e-05 abundance 1530 1220 6.54e-06 2.61e-05
Flavonifractor_plautii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.06 0.233 5.52e-06 2.47e-05 prevalence 1530 1220 6.54e-06 2.61e-05
Anaerostipes_hadrus diagnosis CD diagnosisCD 0.702 0.166 3.59e-06 5.77e-05 abundance 1530 1130 7.18e-06 2.85e-05
Anaerostipes_hadrus diagnosis CD diagnosisCD -0.349 0.175 0.0463 0.0813 prevalence 1530 1130 7.18e-06 2.85e-05
Alistipes_onderdonkii diagnosis CD diagnosisCD -0.121 0.23 1 1 abundance 1530 831 7.61e-06 3.01e-05
Alistipes_onderdonkii diagnosis CD diagnosisCD -0.658 0.142 3.8e-06 1.76e-05 prevalence 1530 831 7.61e-06 3.01e-05
GGB9480_SGB14874 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.14 1.11 0.221 0.424 abundance 1530 332 8.17e-06 3.22e-05
GGB9480_SGB14874 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.32 0.504 4.09e-06 1.88e-05 prevalence 1530 332 8.17e-06 3.22e-05
Phocaeicola_coprocola diagnosis CD diagnosisCD 5.7 2.41 0.0186 0.0611 abundance 1530 101 8.36e-06 3.29e-05
Phocaeicola_coprocola diagnosis CD diagnosisCD 2.79 0.607 4.18e-06 1.91e-05 prevalence 1530 101 8.36e-06 3.29e-05
Acidaminococcus_intestini age age age 0.629 0.174 0.00032 0.00221 abundance 1530 173 8.57e-06 3.35e-05
Barnesiella_intestinihominis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.96 1.04 0.00877 0.0345 abundance 1530 431 8.58e-06 3.35e-05
Acidaminococcus_intestini age age age 0.36 0.0782 4.28e-06 1.95e-05 prevalence 1530 173 8.57e-06 3.35e-05
Barnesiella_intestinihominis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.95 0.425 4.29e-06 1.95e-05 prevalence 1530 431 8.58e-06 3.35e-05
Parasutterella_excrementihominis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.06 0.627 0.0428 0.117 abundance 1530 699 8.85e-06 3.44e-05
Parasutterella_excrementihominis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.24 0.269 4.43e-06 2e-05 prevalence 1530 699 8.85e-06 3.44e-05
Dysosmobacter_sp_BX15 diagnosis UC diagnosisUC -0.909 0.212 4.63e-06 7.31e-05 abundance 1530 621 9.27e-06 3.59e-05
Dysosmobacter_sp_BX15 diagnosis UC diagnosisUC -0.629 0.146 1.61e-05 6.36e-05 prevalence 1530 621 9.27e-06 3.59e-05
Clostridiales_bacterium age age age -0.0272 0.0766 1 1 abundance 1530 985 1.01e-05 3.89e-05
Clostridiales_bacterium age age age 0.291 0.0639 5.05e-06 2.27e-05 prevalence 1530 985 1.01e-05 3.89e-05
Lacrimispora_celerecrescens reads reads reads -0.405 0.0814 1 1 abundance 1530 756 1.12e-05 4.32e-05
Lacrimispora_celerecrescens reads reads reads 0.257 0.0566 5.62e-06 2.51e-05 prevalence 1530 756 1.12e-05 4.32e-05
Coprococcus_comes diagnosis CD diagnosisCD 0.823 0.195 5.66e-06 8.64e-05 abundance 1530 759 1.13e-05 4.34e-05
Coprococcus_comes diagnosis CD diagnosisCD -0.143 0.134 0.288 0.384 prevalence 1530 759 1.13e-05 4.34e-05
Bacteroides_xylanisolvens age age age 0.122 0.126 1 1 abundance 1530 959 1.15e-05 4.38e-05
Bacteroides_xylanisolvens age age age -0.253 0.0558 5.74e-06 2.55e-05 prevalence 1530 959 1.15e-05 4.38e-05
Clostridiales_bacterium diagnosis UC diagnosisUC 0.971 0.197 5.96e-06 8.94e-05 abundance 1530 985 1.19e-05 4.53e-05
Clostridiales_bacterium diagnosis UC diagnosisUC -0.626 0.165 0.000153 0.000487 prevalence 1530 985 1.19e-05 4.53e-05
Prevotella_copri_clade_B age age age 2.92 0.546 6.36e-06 9.38e-05 abundance 1530 40 1.27e-05 4.82e-05
Prevotella_copri_clade_B age age age 0.282 0.139 0.0426 0.0754 prevalence 1530 40 1.27e-05 4.82e-05
GGB33469_SGB15236 diagnosis CD diagnosisCD 0.936 0.341 0.00348 0.0162 abundance 1530 293 1.28e-05 4.82e-05
GGB33469_SGB15236 diagnosis CD diagnosisCD -0.707 0.157 6.38e-06 2.82e-05 prevalence 1530 293 1.28e-05 4.82e-05
Veillonella_rogosae age age age 0.137 0.265 1 1 abundance 1530 207 1.28e-05 4.82e-05
Veillonella_rogosae age age age -0.408 0.0903 6.41e-06 2.82e-05 prevalence 1530 207 1.28e-05 4.82e-05
Roseburia_intestinalis antibiotics Yes antibioticsYes -1.52 0.456 0.00154 0.00858 abundance 1530 842 1.31e-05 4.91e-05
Roseburia_intestinalis antibiotics Yes antibioticsYes -0.838 0.186 6.56e-06 2.87e-05 prevalence 1530 842 1.31e-05 4.91e-05
Clostridium_sp_AM22_11AC diagnosis CD diagnosisCD 1 0.235 6.59e-06 9.57e-05 abundance 1530 730 1.32e-05 4.92e-05
Clostridium_sp_AM22_11AC diagnosis CD diagnosisCD -0.312 0.134 0.0203 0.0394 prevalence 1530 730 1.32e-05 4.92e-05
Faecalibacterium_SGB15315 age age age -0.199 0.137 1 1 abundance 1530 619 1.33e-05 4.93e-05
Faecalibacterium_SGB15315 age age age -0.262 0.0581 6.63e-06 2.9e-05 prevalence 1530 619 1.33e-05 4.93e-05
GGB1680_SGB2312 age age age 1.17 0.269 1.4e-05 5.68e-05 prevalence 1530 12 1.4e-05 5.19e-05
Bacteroides_salyersiae reads reads reads -0.0485 0.223 0.19 0.377 abundance 1530 150 1.47e-05 5.45e-05
Bacteroides_salyersiae reads reads reads 0.377 0.084 7.37e-06 3.21e-05 prevalence 1530 150 1.47e-05 5.45e-05
Faecalibacterium_SGB15315 diagnosis UC diagnosisUC 0.621 0.318 0.0851 0.204 abundance 1530 619 1.5e-05 5.51e-05
Faecalibacterium_SGB15315 diagnosis UC diagnosisUC -0.663 0.148 7.48e-06 3.24e-05 prevalence 1530 619 1.5e-05 5.51e-05
Clostridium_sp_AF36_4 age age age 0.0762 0.0837 1 1 abundance 1530 568 1.51e-05 5.54e-05
Clostridium_sp_AF36_4 age age age 0.25 0.0559 7.54e-06 3.25e-05 prevalence 1530 568 1.51e-05 5.54e-05
Waltera_intestinalis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.7 1.13 0.189 0.377 abundance 1530 524 1.52e-05 5.56e-05
Waltera_intestinalis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.68 0.375 7.6e-06 3.27e-05 prevalence 1530 524 1.52e-05 5.56e-05
Alistipes_dispar antibiotics Yes antibioticsYes 4.67 0.987 7.77e-06 0.000109 abundance 1530 83 1.55e-05 5.66e-05
Alistipes_dispar antibiotics Yes antibioticsYes 0.616 0.323 0.0562 0.0967 prevalence 1530 83 1.55e-05 5.66e-05
Vescimonas_coprocola reads reads reads -0.578 0.107 1 1 abundance 1530 599 1.75e-05 6.37e-05
Vescimonas_coprocola reads reads reads 0.259 0.0583 8.76e-06 3.73e-05 prevalence 1530 599 1.75e-05 6.37e-05
Bacteroides_thetaiotaomicron dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.3 0.84 0.0428 0.117 abundance 1530 1060 1.8e-05 6.52e-05
Bacteroides_thetaiotaomicron dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.59 0.359 9.01e-06 3.83e-05 prevalence 1530 1060 1.8e-05 6.52e-05
Bacteroides_ovatus reads reads reads -0.00272 0.0761 9.2e-06 0.000126 abundance 1530 1180 1.84e-05 6.64e-05
Bacteroides_ovatus reads reads reads 0.278 0.0713 9.5e-05 0.000312 prevalence 1530 1180 1.84e-05 6.64e-05
Alistipes_putredinis age age age -0.304 0.0798 0.000253 0.00184 abundance 1530 873 1.9e-05 6.84e-05
Alistipes_putredinis age age age 0.265 0.0599 9.51e-06 4.02e-05 prevalence 1530 873 1.9e-05 6.84e-05
Phocaeicola_massiliensis diagnosis UC diagnosisUC -1.64 0.381 9.67e-06 0.00013 abundance 1530 396 1.93e-05 6.93e-05
Phocaeicola_massiliensis diagnosis UC diagnosisUC 0.176 0.152 0.246 0.335 prevalence 1530 396 1.93e-05 6.93e-05
Parasutterella_excrementihominis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.87 0.976 0.134 0.29 abundance 1530 699 1.95e-05 6.95e-05
Parasutterella_excrementihominis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.88 0.426 9.74e-06 4.1e-05 prevalence 1530 699 1.95e-05 6.95e-05
Parabacteroides_merdae age age age -0.358 0.0783 1.06e-05 0.00014 abundance 1530 826 2.11e-05 7.51e-05
Parabacteroides_merdae age age age -0.11 0.054 0.0411 0.0731 prevalence 1530 826 2.11e-05 7.51e-05
Clostridium_fessum diagnosis CD diagnosisCD 0.671 0.168 1.15e-05 0.00015 abundance 1530 926 2.29e-05 8.11e-05
Fusicatenibacter_saccharivorans dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.32 0.643 0.155 0.324 abundance 1530 1120 2.3e-05 8.11e-05
Vescimonas_coprocola dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.55 0.824 0.687 1 abundance 1530 599 2.29e-05 8.11e-05
Clostridium_fessum diagnosis CD diagnosisCD -0.443 0.153 0.00374 0.00876 prevalence 1530 926 2.29e-05 8.11e-05
Fusicatenibacter_saccharivorans dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.63 0.372 1.15e-05 4.81e-05 prevalence 1530 1120 2.3e-05 8.11e-05
Vescimonas_coprocola dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.39 0.317 1.14e-05 4.8e-05 prevalence 1530 599 2.29e-05 8.11e-05
Bacteroides_uniformis diagnosis CD diagnosisCD 0.457 0.171 0.00212 0.011 abundance 1530 1240 2.33e-05 8.16e-05
Roseburia_sp_AF02_12 reads reads reads -0.318 0.174 1 1 abundance 1530 363 2.33e-05 8.16e-05
Bacteroides_uniformis diagnosis CD diagnosisCD 0.865 0.197 1.16e-05 4.83e-05 prevalence 1530 1240 2.33e-05 8.16e-05
Roseburia_sp_AF02_12 reads reads reads 0.289 0.066 1.17e-05 4.83e-05 prevalence 1530 363 2.33e-05 8.16e-05
Coprococcus_comes dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.43 1.07 0.00845 0.0334 abundance 1530 759 2.34e-05 8.17e-05
Coprococcus_comes dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.33 0.531 1.17e-05 4.84e-05 prevalence 1530 759 2.34e-05 8.17e-05
Oscillibacter_sp_ER4 antibiotics Yes antibioticsYes -1.55 0.335 1.2e-05 0.000155 abundance 1530 458 2.41e-05 8.37e-05
Oscillibacter_sp_ER4 antibiotics Yes antibioticsYes 0.371 0.198 0.0608 0.102 prevalence 1530 458 2.41e-05 8.37e-05
Lachnospira_eligens age age age 0.365 0.0855 1.22e-05 0.000155 abundance 1530 929 2.44e-05 8.47e-05
Lachnospira_eligens age age age 0.202 0.0585 0.000543 0.00151 prevalence 1530 929 2.44e-05 8.47e-05
Odoribacter_splanchnicus antibiotics Yes antibioticsYes 0.425 0.207 0.0164 0.0557 abundance 1530 757 2.65e-05 9.16e-05
Odoribacter_splanchnicus antibiotics Yes antibioticsYes 0.877 0.201 1.33e-05 5.41e-05 prevalence 1530 757 2.65e-05 9.16e-05
Alistipes_putredinis diagnosis CD diagnosisCD -0.585 0.191 0.00685 0.0283 abundance 1530 873 2.8e-05 9.65e-05
Alistipes_putredinis diagnosis CD diagnosisCD -0.651 0.15 1.4e-05 5.68e-05 prevalence 1530 873 2.8e-05 9.65e-05
Waltera_intestinalis diagnosis UC diagnosisUC -0.178 0.344 0.467 0.738 abundance 1530 524 2.93e-05 0.000101
Waltera_intestinalis diagnosis UC diagnosisUC -0.638 0.147 1.46e-05 5.91e-05 prevalence 1530 524 2.93e-05 0.000101
Phascolarctobacterium_faecium dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.902 0.589 0.246 0.454 abundance 1530 503 3.05e-05 0.000104
Phascolarctobacterium_faecium dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.22 0.281 1.52e-05 6.13e-05 prevalence 1530 503 3.05e-05 0.000104
Bacteroides_fragilis diagnosis UC diagnosisUC 1.42 0.309 1.55e-05 0.000192 abundance 1530 787 3.11e-05 0.000106
Bacteroides_fragilis diagnosis UC diagnosisUC 0.334 0.144 0.0207 0.0402 prevalence 1530 787 3.11e-05 0.000106
GGB9713_SGB15249 diagnosis CD diagnosisCD -0.495 0.348 0.221 0.424 abundance 1530 329 3.13e-05 0.000106
Ruminococcus_bromii diagnosis CD diagnosisCD -0.716 0.271 0.0171 0.0575 abundance 1530 429 3.13e-05 0.000106
GGB9713_SGB15249 diagnosis CD diagnosisCD -0.649 0.15 1.56e-05 6.24e-05 prevalence 1530 329 3.13e-05 0.000106
Ruminococcus_bromii diagnosis CD diagnosisCD -0.609 0.141 1.56e-05 6.24e-05 prevalence 1530 429 3.13e-05 0.000106
Phascolarctobacterium_faecium reads reads reads -0.195 0.11 1 1 abundance 1530 503 3.21e-05 0.000108
Phascolarctobacterium_faecium reads reads reads 0.26 0.0602 1.61e-05 6.36e-05 prevalence 1530 503 3.21e-05 0.000108
Prevotella_stercorea age age age -1.38 0.333 3.26e-05 0.00012 prevalence 1530 40 3.26e-05 0.00011
Prevotella_copri_clade_B diagnosis UC diagnosisUC -7.4 1.48 1.65e-05 2e-04 abundance 1530 40 3.3e-05 0.000111
Prevotella_copri_clade_B diagnosis UC diagnosisUC -1.37 0.515 0.00762 0.0167 prevalence 1530 40 3.3e-05 0.000111
Veillonella_parvula reads reads reads -0.964 0.143 1.67e-05 2e-04 abundance 1530 547 3.34e-05 0.000112
Veillonella_parvula reads reads reads 0.0796 0.0561 0.156 0.23 prevalence 1530 547 3.34e-05 0.000112
Ruminococcus_bicirculans reads reads reads -0.353 0.108 1 1 abundance 1530 678 3.68e-05 0.000123
Ruminococcus_bicirculans reads reads reads 0.24 0.0561 1.84e-05 7.25e-05 prevalence 1530 678 3.68e-05 0.000123
Eisenbergiella_massiliensis diagnosis CD diagnosisCD 0.5 0.404 0.16 0.331 abundance 1530 417 3.8e-05 0.000126
Eisenbergiella_massiliensis diagnosis CD diagnosisCD 0.653 0.153 1.9e-05 7.47e-05 prevalence 1530 417 3.8e-05 0.000126
Bacteroides_finegoldii age age age 0.307 0.188 0.0928 0.218 abundance 1530 333 4.02e-05 0.000133
Coprococcus_comes reads reads reads -0.522 0.0812 1 1 abundance 1530 759 4.02e-05 0.000133
Bacteroides_finegoldii age age age 0.261 0.0613 2.01e-05 7.85e-05 prevalence 1530 333 4.02e-05 0.000133
Coprococcus_comes reads reads reads 0.242 0.0568 2.01e-05 7.85e-05 prevalence 1530 759 4.02e-05 0.000133
Ruminococcus_bromii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.498 0.816 0.381 0.627 abundance 1530 429 4.05e-05 0.000133
Ruminococcus_bromii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.53 0.359 2.02e-05 7.87e-05 prevalence 1530 429 4.05e-05 0.000133
Gemmiger_formicilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.57 0.649 2.04e-05 0.000236 abundance 1530 472 4.08e-05 0.000134
Gemmiger_formicilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.01 0.284 0.000387 0.0011 prevalence 1530 472 4.08e-05 0.000134
Alistipes_shahii reads reads reads 0.0204 0.0846 2.14e-05 0.000243 abundance 1530 673 4.27e-05 0.00014
Alistipes_shahii reads reads reads 0.218 0.0574 0.000149 0.000474 prevalence 1530 673 4.27e-05 0.00014
Acidaminococcus_intestini diagnosis CD diagnosisCD -0.0704 0.524 1 1 abundance 1530 173 4.47e-05 0.000146
Acidaminococcus_intestini diagnosis CD diagnosisCD 0.931 0.219 2.23e-05 8.62e-05 prevalence 1530 173 4.47e-05 0.000146
Dorea_longicatena reads reads reads -0.435 0.0715 1 1 abundance 1530 1020 4.82e-05 0.000156
Lacrimispora_amygdalina dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.328 0.655 0.265 0.476 abundance 1530 865 4.81e-05 0.000156
Dorea_longicatena reads reads reads 0.255 0.0603 2.41e-05 9.23e-05 prevalence 1530 1020 4.82e-05 0.000156
Lacrimispora_amygdalina dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.58 0.374 2.41e-05 9.23e-05 prevalence 1530 865 4.81e-05 0.000156
Ruminococcus_sp_BSD2780120874_150323_B10 diagnosis UC diagnosisUC -1.83 0.451 4.8e-05 0.000171 prevalence 1530 90 4.8e-05 0.000156
Collinsella_aerofaciens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.22 1.22 0.0315 0.0924 abundance 1530 698 4.88e-05 0.000157
Collinsella_aerofaciens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.24 0.531 2.44e-05 9.31e-05 prevalence 1530 698 4.88e-05 0.000157
GGB9713_SGB15249 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.62 1.36 0.0796 0.193 abundance 1530 329 4.96e-05 0.000159
GGB9713_SGB15249 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.15 0.509 2.48e-05 9.43e-05 prevalence 1530 329 4.96e-05 0.000159
Clostridium_sp_AM49_4BH age age age 0.188 0.13 1 1 abundance 1530 344 5.05e-05 0.000162
Clostridium_sp_AM49_4BH age age age 0.27 0.064 2.53e-05 9.57e-05 prevalence 1530 344 5.05e-05 0.000162
Clostridium_symbiosum diagnosis CD diagnosisCD -0.541 0.338 0.164 0.339 abundance 1530 539 5.23e-05 0.000167
Clostridium_symbiosum diagnosis CD diagnosisCD 0.639 0.152 2.62e-05 9.87e-05 prevalence 1530 539 5.23e-05 0.000167
Roseburia_inulinivorans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.00757 0.466 1 1 abundance 1530 951 5.57e-05 0.000177
Roseburia_inulinivorans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.96 0.229 2.79e-05 0.000105 prevalence 1530 951 5.57e-05 0.000177
Ruminococcus_bicirculans diagnosis UC diagnosisUC -0.238 0.245 0.205 0.398 abundance 1530 678 5.62e-05 0.000178
Ruminococcus_bicirculans diagnosis UC diagnosisUC -0.614 0.147 2.81e-05 0.000105 prevalence 1530 678 5.62e-05 0.000178
Veillonella_rogosae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.31 0.596 0.011 0.0412 abundance 1530 207 5.86e-05 0.000185
Veillonella_rogosae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.09 0.261 2.93e-05 0.000109 prevalence 1530 207 5.86e-05 0.000185
Clostridium_fessum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.768 0.882 0.679 1 abundance 1530 926 5.96e-05 0.000188
Clostridium_fessum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.91 0.458 2.98e-05 0.000111 prevalence 1530 926 5.96e-05 0.000188
Prevotella_copri_clade_E age age age -1.32 0.329 6.03e-05 0.000208 prevalence 1530 38 6.03e-05 0.00019
GGB9708_SGB15234 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.0147 1.66 1 1 abundance 1530 282 6.07e-05 0.00019
GGB9708_SGB15234 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.4 0.574 3.04e-05 0.000113 prevalence 1530 282 6.07e-05 0.00019
Roseburia_hominis antibiotics Yes antibioticsYes 0.249 0.383 0.401 0.654 abundance 1530 876 6.26e-05 0.000196
Roseburia_hominis antibiotics Yes antibioticsYes -0.799 0.192 3.13e-05 0.000116 prevalence 1530 876 6.26e-05 0.000196
Bacteroides_finegoldii reads reads reads -1.06 0.188 0.00018 0.00144 abundance 1530 333 6.32e-05 0.000197
Bacteroides_finegoldii reads reads reads 0.274 0.0659 3.16e-05 0.000116 prevalence 1530 333 6.32e-05 0.000197
GGB3746_SGB5089 age age age -0.446 0.104 3.32e-05 0.000352 abundance 1530 651 6.64e-05 0.000206
GGB3746_SGB5089 age age age 0.17 0.0549 0.00199 0.00495 prevalence 1530 651 6.64e-05 0.000206
Firmicutes_bacterium_AF16_15 antibiotics Yes antibioticsYes -0.206 0.393 1 1 abundance 1530 827 6.82e-05 0.000211
Firmicutes_bacterium_AF16_15 antibiotics Yes antibioticsYes -0.865 0.209 3.41e-05 0.000125 prevalence 1530 827 6.82e-05 0.000211
Clostridium_sp_AF20_17LB diagnosis CD diagnosisCD 1.04 0.266 3.47e-05 0.000364 abundance 1530 654 6.95e-05 0.000215
Clostridium_sp_AF20_17LB diagnosis CD diagnosisCD 0.229 0.135 0.0905 0.143 prevalence 1530 654 6.95e-05 0.000215
GGB1543_SGB2126 diagnosis UC diagnosisUC -7.55 1.61 3.64e-05 0.000377 abundance 1530 42 7.29e-05 0.000225
GGB1543_SGB2126 diagnosis UC diagnosisUC -0.784 0.4 0.05 0.0874 prevalence 1530 42 7.29e-05 0.000225
Dysgonomonas_mossii diagnosis CD diagnosisCD -3.59 0.908 7.64e-05 0.000258 prevalence 1530 31 7.64e-05 0.000235
GGB3267_SGB4317 diagnosis CD diagnosisCD -2.71 1 0.0113 0.042 abundance 1530 54 7.95e-05 0.000244
GGB3267_SGB4317 diagnosis CD diagnosisCD -1.86 0.453 3.98e-05 0.000145 prevalence 1530 54 7.95e-05 0.000244
Barnesiella_intestinihominis age age age -0.307 0.119 0.0134 0.0482 abundance 1530 431 8.11e-05 0.000248
Barnesiella_intestinihominis age age age 0.236 0.0574 4.05e-05 0.000147 prevalence 1530 431 8.11e-05 0.000248
Enterocloster_clostridioformis reads reads reads -0.725 0.156 0.0147 0.052 abundance 1530 312 8.36e-05 0.000255
Enterocloster_clostridioformis reads reads reads 0.271 0.0662 4.18e-05 0.000151 prevalence 1530 312 8.36e-05 0.000255
Barnesiella_intestinihominis diagnosis CD diagnosisCD -0.381 0.29 0.282 0.502 abundance 1530 431 8.53e-05 0.000259
Barnesiella_intestinihominis diagnosis CD diagnosisCD -0.578 0.141 4.26e-05 0.000153 prevalence 1530 431 8.53e-05 0.000259
Lacrimispora_celerecrescens diagnosis CD diagnosisCD 0.732 0.195 4.42e-05 0.000447 abundance 1530 756 8.85e-05 0.000267
Roseburia_faecis diagnosis UC diagnosisUC 0.685 0.253 0.0159 0.0546 abundance 1530 922 8.85e-05 0.000267
Lacrimispora_celerecrescens diagnosis CD diagnosisCD -0.403 0.135 0.00286 0.00691 prevalence 1530 756 8.85e-05 0.000267
Roseburia_faecis diagnosis UC diagnosisUC -0.619 0.152 4.42e-05 0.000159 prevalence 1530 922 8.85e-05 0.000267
Roseburia_faecis reads reads reads -0.336 0.0959 1 1 abundance 1530 922 8.94e-05 0.000269
Roseburia_faecis reads reads reads 0.234 0.0574 4.47e-05 0.00016 prevalence 1530 922 8.94e-05 0.000269
Prevotella_sp_885 diagnosis UC diagnosisUC 2.94 2.85 0.318 0.555 abundance 1530 69 9.67e-05 0.00029
Prevotella_sp_885 diagnosis UC diagnosisUC 2.25 0.554 4.84e-05 0.000172 prevalence 1530 69 9.67e-05 0.00029
Tyzzerella_nexilis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.34 0.794 0.241 0.448 abundance 1530 188 9.87e-05 0.000296
Tyzzerella_nexilis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.5 0.369 4.94e-05 0.000174 prevalence 1530 188 9.87e-05 0.000296
Phocaeicola_sartorii diagnosis CD diagnosisCD 1.31 0.336 5.04e-05 0.000504 abundance 1530 424 0.000101 0.000301
Phocaeicola_sartorii diagnosis CD diagnosisCD 0.109 0.157 0.486 0.584 prevalence 1530 424 0.000101 0.000301
GGB3175_SGB4191 diagnosis CD diagnosisCD -1.38 0.521 0.0131 0.0476 abundance 1530 154 0.000104 0.000309
GGB3175_SGB4191 diagnosis CD diagnosisCD -0.778 0.192 5.18e-05 0.000183 prevalence 1530 154 0.000104 0.000309
Proteus_mirabilis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.355 1.32 0.566 0.866 abundance 1530 100 0.000107 0.000316
Proteus_mirabilis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.87 0.464 5.33e-05 0.000187 prevalence 1530 100 0.000107 0.000316
Enterocloster_clostridioformis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.74 0.483 6.33e-05 0.000599 abundance 1530 312 0.000108 0.000318
Enterocloster_clostridioformis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.894 0.221 5.38e-05 0.000188 prevalence 1530 312 0.000108 0.000318
Clostridiales_bacterium dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.431 0.713 1 1 abundance 1530 985 0.000113 0.000334
Clostridiales_bacterium dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.53 0.379 5.66e-05 0.000197 prevalence 1530 985 0.000113 0.000334
GGB3746_SGB5089 diagnosis CD diagnosisCD -0.309 0.248 1 1 abundance 1530 651 0.000115 0.00034
GGB3746_SGB5089 diagnosis CD diagnosisCD -0.547 0.136 5.77e-05 2e-04 prevalence 1530 651 0.000115 0.00034
GGB3746_SGB5089 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.867 0.615 0.0781 0.191 abundance 1530 651 0.000116 0.000341
GGB3746_SGB5089 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.09 0.271 5.8e-05 0.000201 prevalence 1530 651 0.000116 0.000341
Haemophilus_parainfluenzae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.44 0.411 6.12e-05 0.000598 abundance 1530 674 0.000122 0.000358
Haemophilus_parainfluenzae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.442 0.214 0.039 0.07 prevalence 1530 674 0.000122 0.000358
Prevotella_sp_885 diagnosis CD diagnosisCD 4.46 2.65 0.0926 0.218 abundance 1530 69 0.000125 0.000366
Prevotella_sp_885 diagnosis CD diagnosisCD 2.24 0.559 6.27e-05 0.000216 prevalence 1530 69 0.000125 0.000366
Clostridium_leptum age age age -0.403 0.0975 6.35e-05 0.000599 abundance 1530 652 0.000127 0.00037
Clostridium_leptum age age age 0.0906 0.0552 0.101 0.158 prevalence 1530 652 0.000127 0.00037
Roseburia_intestinalis age age age -0.446 0.108 6.39e-05 0.000599 abundance 1530 842 0.000128 0.000371
Roseburia_intestinalis age age age 0.0956 0.0541 0.0774 0.125 prevalence 1530 842 0.000128 0.000371
Bacteroides_faecis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -4.57 1.11 0.000102 0.000874 abundance 1530 434 0.000132 0.000381
Bacteroides_faecis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.29 0.323 6.59e-05 0.000226 prevalence 1530 434 0.000132 0.000381
Bacteroides_salyersiae antibiotics Yes antibioticsYes 1.51 0.577 0.00683 0.0283 abundance 1530 150 0.000138 0.000399
Bacteroides_salyersiae antibiotics Yes antibioticsYes 0.981 0.247 6.9e-05 0.000235 prevalence 1530 150 0.000138 0.000399
Coprococcus_eutactus diagnosis UC diagnosisUC 2.02 0.477 6.93e-05 0.000643 abundance 1530 177 0.000139 0.000399
Coprococcus_eutactus diagnosis UC diagnosisUC -0.711 0.202 0.000428 0.00121 prevalence 1530 177 0.000139 0.000399
Phascolarctobacterium_faecium antibiotics Yes antibioticsYes 0.329 0.346 0.246 0.454 abundance 1530 503 0.000143 0.000412
Phascolarctobacterium_faecium antibiotics Yes antibioticsYes 0.763 0.192 7.17e-05 0.000244 prevalence 1530 503 0.000143 0.000412
Bacteroides_faecis age age age -0.704 0.173 7.31e-05 0.000665 abundance 1530 434 0.000146 0.000419
Bacteroides_faecis age age age 0.00738 0.06 0.902 0.931 prevalence 1530 434 0.000146 0.000419
Faecalibacterium_SGB15315 antibiotics Yes antibioticsYes -1.88 0.588 0.00221 0.0113 abundance 1530 619 0.000158 0.000453
Faecalibacterium_SGB15315 antibiotics Yes antibioticsYes -0.909 0.23 7.92e-05 0.000267 prevalence 1530 619 0.000158 0.000453
GGB1549_SGB2133 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -6.22 1.36 7.99e-05 0.000712 abundance 1530 46 0.00016 0.000455
GGB1549_SGB2133 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.951 0.742 0.2 0.285 prevalence 1530 46 0.00016 0.000455
Dorea_longicatena age age age -0.277 0.0672 8.08e-05 0.000713 abundance 1530 1020 0.000162 0.000459
Dorea_longicatena age age age 0.00183 0.0582 0.975 0.98 prevalence 1530 1020 0.000162 0.000459
Candidatus_Cibionibacter_quicibialis diagnosis UC diagnosisUC 0.256 0.223 1 1 abundance 1530 933 0.000173 0.00049
Phocaeicola_plebeius age age age -0.205 0.258 1 1 abundance 1530 127 0.000173 0.00049
Candidatus_Cibionibacter_quicibialis diagnosis UC diagnosisUC -0.599 0.153 8.66e-05 0.00029 prevalence 1530 933 0.000173 0.00049
Phocaeicola_plebeius age age age 0.335 0.0854 8.67e-05 0.00029 prevalence 1530 127 0.000173 0.00049
Anaerostipes_hadrus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.692 0.536 0.0412 0.114 abundance 1530 1130 0.000175 0.000492
Anaerostipes_hadrus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.35 0.345 8.73e-05 0.000291 prevalence 1530 1130 0.000175 0.000492
Parabacteroides_merdae reads reads reads -0.0214 0.0816 9.23e-05 0.000806 abundance 1530 826 0.000185 0.000519
Parabacteroides_merdae reads reads reads 0.184 0.0562 0.00109 0.00287 prevalence 1530 826 0.000185 0.000519
GGB3746_SGB5089 diagnosis UC diagnosisUC 0.49 0.266 0.116 0.26 abundance 1530 651 0.000189 0.00053
GGB3746_SGB5089 diagnosis UC diagnosisUC -0.574 0.147 9.46e-05 0.000312 prevalence 1530 651 0.000189 0.00053
Clostridiaceae_bacterium diagnosis CD diagnosisCD 0.362 0.16 0.00712 0.0291 abundance 1530 1110 0.00019 0.000531
Clostridiaceae_bacterium diagnosis CD diagnosisCD -0.704 0.18 9.49e-05 0.000312 prevalence 1530 1110 0.00019 0.000531
Veillonella_dispar dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.86 0.53 9.54e-05 0.000826 abundance 1530 526 0.000191 0.000532
Veillonella_dispar dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.453 0.224 0.0432 0.0764 prevalence 1530 526 0.000191 0.000532
Parabacteroides_distasonis diagnosis CD diagnosisCD 0.506 0.148 0.000107 0.000903 abundance 1530 1140 0.000215 0.000597
Parabacteroides_distasonis diagnosis CD diagnosisCD 0.0153 0.161 0.924 0.948 prevalence 1530 1140 0.000215 0.000597
Roseburia_faecis antibiotics Yes antibioticsYes -0.943 0.359 0.0156 0.0543 abundance 1530 922 0.000231 0.000642
Roseburia_faecis antibiotics Yes antibioticsYes -0.706 0.183 0.000116 0.000375 prevalence 1530 922 0.000231 0.000642
Rikenellaceae_bacterium diagnosis CD diagnosisCD -1.15 0.314 0.000234 0.000715 prevalence 1530 67 0.000234 0.000647
Faecalibacterium_prausnitzii reads reads reads -0.232 0.0511 1 1 abundance 1530 1370 0.000238 0.000658
Faecalibacterium_prausnitzii reads reads reads 0.436 0.113 0.000119 0.000385 prevalence 1530 1370 0.000238 0.000658
Enterocloster_clostridioformis diagnosis UC diagnosisUC -1.96 0.522 0.000123 0.00102 abundance 1530 312 0.000245 0.000675
Enterocloster_clostridioformis diagnosis UC diagnosisUC -0.0877 0.198 0.658 0.737 prevalence 1530 312 0.000245 0.000675
GGB16040_SGB9347 diagnosis UC diagnosisUC 1.03 0.717 0.184 0.373 abundance 1530 114 0.00025 0.000685
Phocaeicola_massiliensis diagnosis CD diagnosisCD -0.946 0.398 0.0282 0.085 abundance 1530 396 0.00025 0.000685
GGB16040_SGB9347 diagnosis UC diagnosisUC 1.08 0.282 0.000125 0.000402 prevalence 1530 114 0.00025 0.000685
Phocaeicola_massiliensis diagnosis CD diagnosisCD -0.582 0.152 0.000125 0.000402 prevalence 1530 396 0.00025 0.000685
Phocaeicola_massiliensis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -4.06 0.997 0.000138 0.00114 abundance 1530 396 0.000277 0.000756
Butyrivibrio_crossotus diagnosis CD diagnosisCD -2.25 0.62 0.000278 0.000826 prevalence 1530 43 0.000278 0.000756
Phocaeicola_massiliensis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.03 0.346 0.00293 0.00704 prevalence 1530 396 0.000277 0.000756
Ruminococcus_torques dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.367 0.338 1 1 abundance 1530 1090 0.000292 0.000793
Ruminococcus_torques dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.809 0.213 0.000146 0.000467 prevalence 1530 1090 0.000292 0.000793
Clostridium_symbiosum reads reads reads -0.73 0.117 0.000996 0.00586 abundance 1530 539 0.000306 0.000828
Clostridium_symbiosum reads reads reads 0.215 0.0568 0.000153 0.000487 prevalence 1530 539 0.000306 0.000828
Prevotella_stercorea diagnosis UC diagnosisUC 2.75 0.761 0.000306 0.000901 prevalence 1530 40 0.000306 0.000828
Sutterella_wadsworthensis diagnosis UC diagnosisUC -0.504 0.228 0.0117 0.0428 abundance 1530 536 0.000308 0.000831
Sutterella_wadsworthensis diagnosis UC diagnosisUC -0.574 0.152 0.000154 0.000488 prevalence 1530 536 0.000308 0.000831
Blautia_wexlerae diagnosis CD diagnosisCD 0.555 0.164 0.000155 0.00127 abundance 1530 1300 0.000309 0.000832
Blautia_wexlerae diagnosis CD diagnosisCD -0.378 0.229 0.0994 0.156 prevalence 1530 1300 0.000309 0.000832
Clostridium_sp_AF36_4 antibiotics Yes antibioticsYes -1.05 0.421 0.0211 0.0682 abundance 1530 568 0.00033 0.000884
Clostridium_sp_AF36_4 antibiotics Yes antibioticsYes -0.857 0.227 0.000165 0.00052 prevalence 1530 568 0.00033 0.000884
Dysosmobacter_sp_BX15 reads reads reads -0.0829 0.0907 1 1 abundance 1530 621 0.000348 0.00093
Dysosmobacter_sp_BX15 reads reads reads 0.214 0.0569 0.000174 0.000547 prevalence 1530 621 0.000348 0.00093
Eisenbergiella_massiliensis age age age -0.645 0.168 0.000176 0.00141 abundance 1530 417 0.000352 0.00094
Eisenbergiella_massiliensis age age age 0.069 0.0591 0.243 0.333 prevalence 1530 417 0.000352 0.00094
Prevotella_copri_clade_B diagnosis CD diagnosisCD -5.63 1.32 0.000185 0.00145 abundance 1530 40 0.00037 0.000985
Prevotella_copri_clade_B diagnosis CD diagnosisCD -0.342 0.35 0.329 0.427 prevalence 1530 40 0.00037 0.000985
Bacteroides_eggerthii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -4.79 3.31 0.168 0.346 abundance 1530 409 0.000375 0.000995
Bacteroides_eggerthii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.55 0.683 0.000188 0.000588 prevalence 1530 409 0.000375 0.000995
Prevotella_copri_clade_E diagnosis UC diagnosisUC 2.71 0.762 0.000376 0.00107 prevalence 1530 38 0.000376 0.000995
Hungatella_hathewayi dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.75 0.524 0.000191 0.00148 abundance 1530 451 0.000382 0.00101
Hungatella_hathewayi dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.362 0.216 0.0941 0.149 prevalence 1530 451 0.000382 0.00101
Collinsella_aerofaciens reads reads reads -0.459 0.0919 1 1 abundance 1530 698 0.000384 0.00101
Collinsella_aerofaciens reads reads reads 0.207 0.0554 0.000192 0.000601 prevalence 1530 698 0.000384 0.00101
Paraprevotella_clara dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -6.6 1.67 0.000193 0.00149 abundance 1530 178 0.000386 0.00102
Paraprevotella_clara dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.54 0.577 0.00765 0.0167 prevalence 1530 178 0.000386 0.00102
Lachnospira_pectinoschiza dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.18 0.686 0.0423 0.116 abundance 1530 500 0.000389 0.00102
Lachnospira_pectinoschiza dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.12 0.3 0.000195 0.000607 prevalence 1530 500 0.000389 0.00102
Acidaminococcus_intestini antibiotics Yes antibioticsYes -1.35 0.488 0.00945 0.0365 abundance 1530 173 0.00041 0.00107
Acidaminococcus_intestini antibiotics Yes antibioticsYes 0.836 0.225 0.000205 0.000637 prevalence 1530 173 0.00041 0.00107
Blautia_obeum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.18 0.681 0.253 0.463 abundance 1530 899 0.00042 0.0011
Blautia_obeum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.31 0.353 0.00021 0.000651 prevalence 1530 899 0.00042 0.0011
Alistipes_putredinis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.719 1.21 0.353 0.592 abundance 1530 873 0.000424 0.0011
Alistipes_putredinis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.97 0.532 0.000212 0.000655 prevalence 1530 873 0.000424 0.0011
Dysosmobacter_sp_BX15 diagnosis CD diagnosisCD -0.0537 0.194 1 1 abundance 1530 621 0.000432 0.00112
Dysosmobacter_sp_BX15 diagnosis CD diagnosisCD -0.495 0.134 0.000216 0.000666 prevalence 1530 621 0.000432 0.00112
Phocaeicola_dorei dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.0661 0.998 0.776 1 abundance 1530 769 0.000448 0.00116
Phocaeicola_dorei dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.879 0.238 0.000224 0.000689 prevalence 1530 769 0.000448 0.00116
Fusicatenibacter_saccharivorans age age age -0.106 0.0685 1 1 abundance 1530 1120 0.000457 0.00118
Fusicatenibacter_saccharivorans age age age 0.261 0.0709 0.000228 7e-04 prevalence 1530 1120 0.000457 0.00118
GGB9480_SGB14874 age age age -0.448 0.117 0.000231 0.00172 abundance 1530 332 0.000461 0.00119
GGB9480_SGB14874 age age age 0.222 0.0618 0.000333 0.000972 prevalence 1530 332 0.000461 0.00119
Parasutterella_excrementihominis reads reads reads -0.378 0.102 1 1 abundance 1530 699 0.000474 0.00122
Veillonella_dispar diagnosis CD diagnosisCD -1.15 0.342 0.00171 0.00919 abundance 1530 526 0.000475 0.00122
Parasutterella_excrementihominis reads reads reads 0.205 0.0559 0.000237 0.000722 prevalence 1530 699 0.000474 0.00122
Veillonella_dispar diagnosis CD diagnosisCD -0.525 0.143 0.000238 0.000722 prevalence 1530 526 0.000475 0.00122
Anaerostipes_hadrus reads reads reads -0.481 0.0709 1 1 abundance 1530 1130 0.000486 0.00124
Anaerostipes_hadrus reads reads reads 0.245 0.0668 0.000243 0.000735 prevalence 1530 1130 0.000486 0.00124
Ruthenibacterium_lactatiformans age age age -0.00639 0.0959 1 1 abundance 1530 797 0.000494 0.00126
Ruthenibacterium_lactatiformans age age age 0.201 0.0548 0.000247 0.000746 prevalence 1530 797 0.000494 0.00126
Clostridium_sp_AT4 age age age 0.407 0.113 0.000251 0.00184 abundance 1530 528 0.000502 0.00128
Clostridium_sp_AT4 age age age -0.0376 0.0577 0.514 0.612 prevalence 1530 528 0.000502 0.00128
Bifidobacterium_adolescentis age age age 0.0641 0.151 1 1 abundance 1530 427 0.000508 0.00129
Bifidobacterium_adolescentis age age age -0.227 0.062 0.000254 0.000766 prevalence 1530 427 0.000508 0.00129
GGB1266_SGB1699 diagnosis UC diagnosisUC -1.47 0.932 0.103 0.237 abundance 1530 84 0.000524 0.00133
GGB1266_SGB1699 diagnosis UC diagnosisUC 1.17 0.321 0.000262 0.000786 prevalence 1530 84 0.000524 0.00133
GGB3278_SGB4328 diagnosis UC diagnosisUC -0.989 0.501 0.0356 0.103 abundance 1530 179 0.000545 0.00138
GGB3278_SGB4328 diagnosis UC diagnosisUC -0.749 0.206 0.000272 0.000816 prevalence 1530 179 0.000545 0.00138
Bacteroides_fragilis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 2.69 0.625 0.000277 0.002 abundance 1530 787 0.000554 0.00139
Clostridiaceae_bacterium_Marseille_Q4149 diagnosis CD diagnosisCD 0.472 0.563 0.338 0.58 abundance 1530 181 0.000553 0.00139
Bacteroides_fragilis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.498 0.336 0.139 0.208 prevalence 1530 787 0.000554 0.00139
Clostridiaceae_bacterium_Marseille_Q4149 diagnosis CD diagnosisCD -0.751 0.207 0.000277 0.000826 prevalence 1530 181 0.000553 0.00139
Bacteroides_ovatus diagnosis CD diagnosisCD 0.623 0.19 0.000281 0.002 abundance 1530 1180 0.000562 0.00141
Bacteroides_ovatus diagnosis CD diagnosisCD 0.182 0.165 0.268 0.36 prevalence 1530 1180 0.000562 0.00141
Lacrimispora_amygdalina diagnosis CD diagnosisCD 0.591 0.181 0.000283 0.002 abundance 1530 865 0.000565 0.00142
Lacrimispora_amygdalina diagnosis CD diagnosisCD -0.51 0.143 0.000363 0.00105 prevalence 1530 865 0.000565 0.00142
Haemophilus_parainfluenzae antibiotics Yes antibioticsYes 0.79 0.434 0.0473 0.128 abundance 1530 674 0.00057 0.00142
Haemophilus_parainfluenzae antibiotics Yes antibioticsYes -0.714 0.197 0.000285 0.000846 prevalence 1530 674 0.00057 0.00142
Clostridium_sp_AF34_10BH age age age 0.299 0.0851 0.000292 0.00205 abundance 1530 960 0.000584 0.00146
Clostridium_sp_AF34_10BH age age age 0.118 0.0614 0.0539 0.0934 prevalence 1530 960 0.000584 0.00146
Faecalibacterium_prausnitzii antibiotics Yes antibioticsYes -0.201 0.186 1 1 abundance 1530 1370 0.00059 0.00147
Faecalibacterium_prausnitzii antibiotics Yes antibioticsYes -1.01 0.279 0.000295 0.000873 prevalence 1530 1370 0.00059 0.00147
Candidatus_Cibionibacter_quicibialis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.888 0.805 0.109 0.249 abundance 1530 933 0.000593 0.00147
Candidatus_Cibionibacter_quicibialis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.37 0.379 0.000297 0.000876 prevalence 1530 933 0.000593 0.00147
Dysgonomonas_mossii diagnosis UC diagnosisUC -9 3.81 0.0254 0.0798 abundance 1530 31 0.000621 0.00154
Dysgonomonas_mossii diagnosis UC diagnosisUC -1.85 0.513 0.000311 0.000912 prevalence 1530 31 0.000621 0.00154
Bacteroides_intestinalis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.77 1.49 0.018 0.0598 abundance 1530 158 0.000642 0.00159
Bacteroides_intestinalis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.89 0.525 0.000321 0.00094 prevalence 1530 158 0.000642 0.00159
Bacteroides_fragilis antibiotics Yes antibioticsYes -1.24 0.407 0.0044 0.0196 abundance 1530 787 0.000675 0.00166
Bacteroides_fragilis antibiotics Yes antibioticsYes -0.655 0.183 0.000337 0.000982 prevalence 1530 787 0.000675 0.00166
Alistipes_onderdonkii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.782 2.8 0.892 1 abundance 1530 831 0.000681 0.00167
Alistipes_onderdonkii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -3.49 0.973 0.000341 0.000989 prevalence 1530 831 0.000681 0.00167
Gemmiger_formicilis reads reads reads -0.58 0.123 1 1 abundance 1530 472 0.000698 0.00171
Gemmiger_formicilis reads reads reads 0.216 0.0603 0.000349 0.00101 prevalence 1530 472 0.000698 0.00171
Parasutterella_excrementihominis antibiotics Yes antibioticsYes -0.386 0.336 0.352 0.592 abundance 1530 699 0.000728 0.00178
Parasutterella_excrementihominis antibiotics Yes antibioticsYes 0.672 0.188 0.000364 0.00105 prevalence 1530 699 0.000728 0.00178
Ruminococcus_bicirculans age age age 0.214 0.0963 1 1 abundance 1530 678 0.000733 0.00179
Ruminococcus_bicirculans age age age 0.194 0.0545 0.000366 0.00105 prevalence 1530 678 0.000733 0.00179
Clostridiaceae_bacterium_Marseille_Q4149 age age age 0.294 0.207 0.142 0.302 abundance 1530 181 0.000738 0.0018
Clostridiaceae_bacterium_Marseille_Q4149 age age age 0.262 0.0736 0.000369 0.00106 prevalence 1530 181 0.000738 0.0018
Bacteroides_intestinalis antibiotics Yes antibioticsYes 2.42 0.686 0.000385 0.00263 abundance 1530 158 0.000771 0.00187
Roseburia_intestinalis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 1.59 0.507 0.000385 0.00263 abundance 1530 842 0.000771 0.00187
Bacteroides_intestinalis antibiotics Yes antibioticsYes 0.72 0.251 0.00412 0.00956 prevalence 1530 158 0.000771 0.00187
Roseburia_intestinalis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.405 0.214 0.0576 0.0982 prevalence 1530 842 0.000771 0.00187
Enterocloster_clostridioformis diagnosis CD diagnosisCD 0.793 0.429 0.0456 0.124 abundance 1530 312 0.000782 0.00189
Enterocloster_clostridioformis diagnosis CD diagnosisCD 0.609 0.172 0.000391 0.00111 prevalence 1530 312 0.000782 0.00189
Dorea_longicatena dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.417 0.553 0.138 0.297 abundance 1530 1020 0.000795 0.00192
Dorea_longicatena dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.22 0.344 0.000397 0.00113 prevalence 1530 1020 0.000795 0.00192
GGB3278_SGB4328 age age age -0.729 0.199 0.000412 0.00277 abundance 1530 179 0.000824 0.00198
GGB3278_SGB4328 age age age 0.02 0.0787 0.8 0.846 prevalence 1530 179 0.000824 0.00198
Alistipes_dispar dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 8.43 2.17 0.000423 0.00282 abundance 1530 83 0.000846 0.00203
Alistipes_dispar dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.168 1.02 0.869 0.904 prevalence 1530 83 0.000846 0.00203
Bifidobacterium_adolescentis antibiotics Yes antibioticsYes -1.92 0.747 0.014 0.0499 abundance 1530 427 0.000923 0.00221
Bifidobacterium_adolescentis antibiotics Yes antibioticsYes -0.997 0.285 0.000462 0.0013 prevalence 1530 427 0.000923 0.00221
Dialister_invisus diagnosis UC diagnosisUC -0.788 0.245 0.000472 0.0031 abundance 1530 726 0.000945 0.00226
Dialister_invisus diagnosis UC diagnosisUC 0.0926 0.147 0.53 0.625 prevalence 1530 726 0.000945 0.00226
Veillonella_parvula diagnosis CD diagnosisCD 0.572 0.343 0.0619 0.16 abundance 1530 547 0.000965 0.0023
Veillonella_parvula diagnosis CD diagnosisCD -0.488 0.14 0.000483 0.00136 prevalence 1530 547 0.000965 0.0023
Akkermansia_muciniphila antibiotics Yes antibioticsYes -0.145 0.71 1 1 abundance 1530 407 0.000973 0.00232
Akkermansia_muciniphila antibiotics Yes antibioticsYes -0.871 0.25 0.000487 0.00137 prevalence 1530 407 0.000973 0.00232
Klebsiella_pneumoniae antibiotics Yes antibioticsYes 2.29 0.657 0.000488 0.00318 abundance 1530 119 0.000976 0.00232
Klebsiella_pneumoniae antibiotics Yes antibioticsYes 0.559 0.264 0.0342 0.0627 prevalence 1530 119 0.000976 0.00232
Bacteroides_finegoldii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.23 1.54 0.192 0.381 abundance 1530 333 0.000983 0.00233
Bacteroides_finegoldii dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.64 0.47 0.000492 0.00137 prevalence 1530 333 0.000983 0.00233
Veillonella_dispar reads reads reads -0.847 0.144 0.000496 0.00321 abundance 1530 526 0.000991 0.00234
Veillonella_dispar reads reads reads 0.00485 0.0571 0.932 0.952 prevalence 1530 526 0.000991 0.00234
Alistipes_finegoldii reads reads reads 0.0511 0.112 0.000502 0.00323 abundance 1530 639 0.001 0.00237
Alistipes_finegoldii reads reads reads 0.144 0.0567 0.0112 0.0233 prevalence 1530 639 0.001 0.00237
Bacteroides_caecigallinarum diagnosis CD diagnosisCD 6.73 7.47 0.378 0.625 abundance 1530 21 0.00103 0.00242
Bifidobacterium_adolescentis diagnosis UC diagnosisUC 1.2 0.322 0.000515 0.00329 abundance 1530 427 0.00103 0.00242
Bacteroides_caecigallinarum diagnosis CD diagnosisCD -2.51 0.722 0.000515 0.00144 prevalence 1530 21 0.00103 0.00242
Bifidobacterium_adolescentis diagnosis UC diagnosisUC -0.242 0.149 0.105 0.162 prevalence 1530 427 0.00103 0.00242
Akkermansia_sp_KLE1798 reads reads reads 0.413 0.126 0.00105 0.00275 prevalence 1530 70 0.00105 0.00245
Rikenellaceae_bacterium reads reads reads 0.386 0.118 0.00105 0.00277 prevalence 1530 67 0.00105 0.00246
Bacteroides_xylanisolvens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.527 1.06 0.381 0.627 abundance 1530 959 0.00106 0.00246
Bacteroides_xylanisolvens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.25 0.36 0.000528 0.00147 prevalence 1530 959 0.00106 0.00246
Veillonella_rogosae antibiotics Yes antibioticsYes 2.98 0.867 0.000537 0.0034 abundance 1530 207 0.00107 0.0025
Veillonella_rogosae antibiotics Yes antibioticsYes -0.965 0.342 0.00474 0.0108 prevalence 1530 207 0.00107 0.0025
Eubacterium_siraeum diagnosis CD diagnosisCD -1.19 0.322 0.00054 0.0034 abundance 1530 565 0.00108 0.00251
Eubacterium_siraeum diagnosis CD diagnosisCD -0.456 0.135 0.000761 0.00205 prevalence 1530 565 0.00108 0.00251
Clostridium_sp_AF34_10BH dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.81 0.787 0.075 0.185 abundance 1530 960 0.00112 0.00259
Clostridium_sp_AF34_10BH dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.28 0.371 0.000559 0.00155 prevalence 1530 960 0.00112 0.00259
Bacteroides_xylanisolvens diagnosis CD diagnosisCD -0.0686 0.284 1 1 abundance 1530 959 0.00117 0.00271
Bacteroides_xylanisolvens diagnosis CD diagnosisCD 0.503 0.146 0.000585 0.00162 prevalence 1530 959 0.00117 0.00271
Bacteroides_fragilis reads reads reads -0.357 0.108 1 1 abundance 1530 787 0.00118 0.00272
Bacteroides_fragilis reads reads reads 0.187 0.0545 0.00059 0.00163 prevalence 1530 787 0.00118 0.00272
Roseburia_faecis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.582 0.411 0.376 0.623 abundance 1530 922 0.00127 0.00293
Roseburia_faecis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.726 0.212 0.000635 0.00174 prevalence 1530 922 0.00127 0.00293
Lachnospira_eligens diagnosis CD diagnosisCD 0.201 0.214 0.206 0.399 abundance 1530 929 0.00136 0.00313
Lachnospira_eligens diagnosis CD diagnosisCD -0.48 0.141 0.00068 0.00186 prevalence 1530 929 0.00136 0.00313
Ruminococcus_lactaris reads reads reads -0.286 0.127 1 1 abundance 1530 379 0.00138 0.00316
Ruminococcus_lactaris reads reads reads 0.215 0.0633 0.000689 0.00188 prevalence 1530 379 0.00138 0.00316
Lacrimispora_celerecrescens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.798 0.631 0.532 0.824 abundance 1530 756 0.0014 0.00321
Lacrimispora_celerecrescens dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.22 0.359 0.000701 0.00191 prevalence 1530 756 0.0014 0.00321
Alistipes_shahii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.794 1.45 0.787 1 abundance 1530 673 0.00143 0.00326
Roseburia_intestinalis diagnosis CD diagnosisCD -0.169 0.273 1 1 abundance 1530 842 0.00143 0.00326
Alistipes_shahii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.43 0.717 0.000715 0.00194 prevalence 1530 673 0.00143 0.00326
Roseburia_intestinalis diagnosis CD diagnosisCD -0.457 0.135 0.000715 0.00194 prevalence 1530 842 0.00143 0.00326
Bilophila_wadsworthia age age age -0.278 0.0789 0.000753 0.00464 abundance 1530 764 0.00151 0.00342
Bilophila_wadsworthia age age age 0.176 0.0562 0.00179 0.00452 prevalence 1530 764 0.00151 0.00342
Dialister_invisus diagnosis CD diagnosisCD -0.0691 0.216 1 1 abundance 1530 726 0.00152 0.00345
Dialister_invisus diagnosis CD diagnosisCD 0.46 0.137 0.000762 0.00205 prevalence 1530 726 0.00152 0.00345
GGB781_SGB1024 age age age 0.598 0.189 0.00152 0.00393 prevalence 1530 18 0.00152 0.00345
Alistipes_communis antibiotics Yes antibioticsYes -0.0777 0.485 1 1 abundance 1530 407 0.00154 0.00347
Alistipes_communis antibiotics Yes antibioticsYes -0.824 0.245 0.000768 0.00207 prevalence 1530 407 0.00154 0.00347
Odoribacter_splanchnicus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.435 1.27 1 1 abundance 1530 757 0.00155 0.00349
Odoribacter_splanchnicus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.42 0.719 0.000774 0.00208 prevalence 1530 757 0.00155 0.00349
Bifidobacterium_longum diagnosis UC diagnosisUC 0.00133 0.244 1 1 abundance 1530 843 0.00159 0.00358
Lachnospira_pectinoschiza antibiotics Yes antibioticsYes -1.57 0.501 0.00291 0.014 abundance 1530 500 0.00159 0.00358
Bifidobacterium_longum diagnosis UC diagnosisUC 0.523 0.156 0.000796 0.00213 prevalence 1530 843 0.00159 0.00358
Lachnospira_pectinoschiza antibiotics Yes antibioticsYes -0.762 0.227 0.000797 0.00213 prevalence 1530 500 0.00159 0.00358
Bacteroides_caecigallinarum diagnosis UC diagnosisUC -9.26 2.2 0.000811 0.0049 abundance 1530 21 0.00162 0.00363
Bacteroides_caecigallinarum diagnosis UC diagnosisUC -1.42 0.571 0.0128 0.0266 prevalence 1530 21 0.00162 0.00363
Alistipes_putredinis reads reads reads -0.194 0.0819 1 1 abundance 1530 873 0.00173 0.00386
Alistipes_putredinis reads reads reads 0.197 0.0593 0.000865 0.0023 prevalence 1530 873 0.00173 0.00386
Bilophila_wadsworthia dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.812 2.26 0.591 0.899 abundance 1530 764 0.00176 0.00392
Bilophila_wadsworthia dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -3.25 0.977 0.000879 0.00233 prevalence 1530 764 0.00176 0.00392
Phocaeicola_coprocola antibiotics Yes antibioticsYes -4.66 1.34 0.000899 0.00539 abundance 1530 101 0.0018 0.004
Phocaeicola_coprocola antibiotics Yes antibioticsYes -0.597 0.402 0.138 0.207 prevalence 1530 101 0.0018 0.004
Phocaeicola_vulgatus reads reads reads -0.193 0.0985 1 1 abundance 1530 1290 0.00184 0.00408
Phocaeicola_vulgatus reads reads reads 0.267 0.0804 0.00092 0.00244 prevalence 1530 1290 0.00184 0.00408
Bifidobacterium_adolescentis reads reads reads -0.629 0.14 0.0408 0.113 abundance 1530 427 0.00199 0.00442
Bifidobacterium_adolescentis reads reads reads 0.202 0.0614 0.000997 0.00263 prevalence 1530 427 0.00199 0.00442
Prevotella_copri_clade_A diagnosis CD diagnosisCD -2.36 0.694 0.00109 0.00635 abundance 1530 289 0.00217 0.0048
Prevotella_copri_clade_A diagnosis CD diagnosisCD -0.481 0.164 0.00336 0.00797 prevalence 1530 289 0.00217 0.0048
Ruminococcus_bicirculans antibiotics Yes antibioticsYes -1.06 0.443 0.0259 0.0802 abundance 1530 678 0.00221 0.00487
Ruminococcus_bicirculans antibiotics Yes antibioticsYes -0.651 0.2 0.0011 0.00289 prevalence 1530 678 0.00221 0.00487
Phocaeicola_coprocola dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -5.44 1.56 0.00114 0.00663 abundance 1530 101 0.00228 0.00503
Phocaeicola_coprocola dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.775 0.474 0.102 0.159 prevalence 1530 101 0.00228 0.00503
Barnesiella_intestinihominis reads reads reads 0.0409 0.132 0.00385 0.0178 abundance 1530 431 0.00237 0.0052
Barnesiella_intestinihominis reads reads reads 0.197 0.0608 0.00118 0.00309 prevalence 1530 431 0.00237 0.0052
Alistipes_finegoldii age age age -0.349 0.104 0.00122 0.00701 abundance 1530 639 0.00244 0.00536
Alistipes_finegoldii age age age -0.0693 0.0554 0.211 0.297 prevalence 1530 639 0.00244 0.00536
Ruminococcus_lactaris dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.741 1.22 0.433 0.697 abundance 1530 379 0.00271 0.00593
Ruminococcus_lactaris dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.63 0.508 0.00136 0.00353 prevalence 1530 379 0.00271 0.00593
Acidaminococcus_intestini dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.372 0.853 0.489 0.766 abundance 1530 173 0.00272 0.00595
Acidaminococcus_intestini dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.19 0.372 0.00136 0.00354 prevalence 1530 173 0.00272 0.00595
Candidatus_Cibionibacter_quicibialis age age age 0.261 0.0846 0.00137 0.00775 abundance 1530 933 0.00274 0.00597
Candidatus_Cibionibacter_quicibialis age age age 0.108 0.0573 0.0603 0.101 prevalence 1530 933 0.00274 0.00597
GGB51647_SGB4348 diagnosis CD diagnosisCD 0.566 0.61 0.3 0.527 abundance 1530 123 0.0028 0.00608
GGB51647_SGB4348 diagnosis CD diagnosisCD -0.758 0.237 0.0014 0.00363 prevalence 1530 123 0.0028 0.00608
Odoribacter_splanchnicus diagnosis CD diagnosisCD 0.418 0.152 0.00145 0.00813 abundance 1530 757 0.00291 0.00631
Odoribacter_splanchnicus diagnosis CD diagnosisCD -0.2 0.136 0.142 0.212 prevalence 1530 757 0.00291 0.00631
Dysosmobacter_sp_BX15 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.85 1.02 0.0271 0.0832 abundance 1530 621 0.00311 0.00674
Dysosmobacter_sp_BX15 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.69 0.533 0.00156 0.00401 prevalence 1530 621 0.00311 0.00674
Alistipes_SGB2313 diagnosis CD diagnosisCD -2.83 0.837 0.00157 0.00868 abundance 1530 73 0.00314 0.00679
Alistipes_SGB2313 diagnosis CD diagnosisCD -0.548 0.307 0.0744 0.121 prevalence 1530 73 0.00314 0.00679
Prevotella_marseillensis antibiotics Yes antibioticsYes 1.6 0.543 0.00321 0.00768 prevalence 1530 18 0.00321 0.00693
Bifidobacterium_longum reads reads reads -0.645 0.0959 0.00161 0.00875 abundance 1530 843 0.00323 0.00694
Bifidobacterium_longum reads reads reads 0.171 0.057 0.00262 0.00635 prevalence 1530 843 0.00323 0.00694
GGB3478_SGB14857 antibiotics Yes antibioticsYes 5.02 1.77 0.0182 0.0599 abundance 1530 16 0.00324 0.00696
GGB3478_SGB14857 antibiotics Yes antibioticsYes 1.58 0.501 0.00162 0.00417 prevalence 1530 16 0.00324 0.00696
Parasutterella_SGB9260 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.65 1.28 0.0579 0.153 abundance 1530 269 0.00325 0.00697
Parasutterella_SGB9260 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.81 0.574 0.00163 0.00417 prevalence 1530 269 0.00325 0.00697
Clostridium_leptum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.706 0.973 0.756 1 abundance 1530 652 0.00339 0.00726
Clostridium_leptum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.35 0.43 0.0017 0.00433 prevalence 1530 652 0.00339 0.00726
Clostridium_fessum antibiotics Yes antibioticsYes -0.435 0.283 0.2 0.393 abundance 1530 926 0.00342 0.00729
Clostridium_fessum antibiotics Yes antibioticsYes -0.62 0.198 0.00171 0.00435 prevalence 1530 926 0.00342 0.00729
Phocaeicola_massiliensis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.0915 1.77 0.78 1 abundance 1530 396 0.00347 0.00739
Phocaeicola_massiliensis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.88 0.601 0.00173 0.00441 prevalence 1530 396 0.00347 0.00739
Bacteroides_thetaiotaomicron antibiotics Yes antibioticsYes 0.991 0.339 0.00174 0.00935 abundance 1530 1060 0.00349 0.00741
Bacteroides_thetaiotaomicron antibiotics Yes antibioticsYes -0.0976 0.204 0.632 0.714 prevalence 1530 1060 0.00349 0.00741
Haemophilus_parainfluenzae diagnosis CD diagnosisCD -0.184 0.263 1 1 abundance 1530 674 0.00351 0.00745
Parasutterella_excrementihominis diagnosis UC diagnosisUC 0.836 0.243 0.00176 0.00935 abundance 1530 699 0.00351 0.00745
Haemophilus_parainfluenzae diagnosis CD diagnosisCD -0.427 0.137 0.00176 0.00446 prevalence 1530 674 0.00351 0.00745
Parasutterella_excrementihominis diagnosis UC diagnosisUC 0.0636 0.145 0.66 0.738 prevalence 1530 699 0.00351 0.00745
Waltera_intestinalis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.06 2.23 0.767 1 abundance 1530 524 0.00363 0.00767
Waltera_intestinalis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.24 0.719 0.00182 0.00458 prevalence 1530 524 0.00363 0.00767
Alistipes_dispar diagnosis UC diagnosisUC -1.12 0.739 0.111 0.253 abundance 1530 83 0.00364 0.00767
Alistipes_dispar diagnosis UC diagnosisUC -1.11 0.356 0.00182 0.00458 prevalence 1530 83 0.00364 0.00767
GGB9480_SGB14874 diagnosis UC diagnosisUC -0.279 0.349 0.314 0.549 abundance 1530 332 0.00374 0.00787
GGB9480_SGB14874 diagnosis UC diagnosisUC -0.557 0.179 0.00187 0.0047 prevalence 1530 332 0.00374 0.00787
Flavonifractor_plautii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.01 0.485 0.211 0.407 abundance 1530 1220 0.00376 0.00789
Flavonifractor_plautii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.14 0.366 0.00188 0.00471 prevalence 1530 1220 0.00376 0.00789
Escherichia_coli age age age 0.361 0.119 0.00191 0.00998 abundance 1530 707 0.00381 0.00799
Escherichia_coli age age age -0.0974 0.0537 0.0698 0.115 prevalence 1530 707 0.00381 0.00799
Ruminococcus_gnavus diagnosis UC diagnosisUC -0.495 0.289 0.0498 0.134 abundance 1530 767 0.00387 0.0081
Ruminococcus_gnavus diagnosis UC diagnosisUC 0.455 0.147 0.00194 0.00484 prevalence 1530 767 0.00387 0.0081
Bifidobacterium_adolescentis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.41 1.61 0.261 0.471 abundance 1530 427 0.0039 0.00815
Bifidobacterium_adolescentis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.87 0.603 0.00195 0.00487 prevalence 1530 427 0.0039 0.00815
Akkermansia_muciniphila reads reads reads -0.481 0.16 1 1 abundance 1530 407 0.00398 0.00831
Akkermansia_muciniphila reads reads reads 0.193 0.0624 0.00199 0.00495 prevalence 1530 407 0.00398 0.00831
Veillonella_rogosae reads reads reads -0.987 0.207 0.00207 0.0107 abundance 1530 207 0.00413 0.00858
Veillonella_rogosae reads reads reads 0.0304 0.0778 0.696 0.768 prevalence 1530 207 0.00413 0.00858
Proteus_mirabilis diagnosis CD diagnosisCD -1.64 0.864 0.0722 0.18 abundance 1530 100 0.00414 0.00859
Vescimonas_coprocola dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.45 1.39 0.181 0.369 abundance 1530 599 0.00415 0.00859
Proteus_mirabilis diagnosis CD diagnosisCD -0.874 0.284 0.00207 0.00513 prevalence 1530 100 0.00414 0.00859
Vescimonas_coprocola dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.85 0.602 0.00208 0.00513 prevalence 1530 599 0.00415 0.00859
Waltera_intestinalis age age age 0.389 0.139 0.00418 0.0189 abundance 1530 524 0.00418 0.00864
Waltera_intestinalis age age age 0.172 0.0559 0.00209 0.00515 prevalence 1530 524 0.00418 0.00864
Bacteroides_faecis antibiotics Yes antibioticsYes -1.41 0.77 0.0836 0.201 abundance 1530 434 0.00435 0.00898
Bacteroides_faecis antibiotics Yes antibioticsYes -0.737 0.24 0.00218 0.00535 prevalence 1530 434 0.00435 0.00898
Clostridium_sp_AM49_4BH antibiotics Yes antibioticsYes -0.118 0.829 1 1 abundance 1530 344 0.00447 0.00921
Clostridium_sp_AM49_4BH antibiotics Yes antibioticsYes -1.05 0.342 0.00224 0.00549 prevalence 1530 344 0.00447 0.00921
Clostridium_sp_AM22_11AC dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.02 0.796 0.441 0.704 abundance 1530 730 0.00457 0.00939
Clostridium_sp_AM22_11AC dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.16 0.381 0.00229 0.00559 prevalence 1530 730 0.00457 0.00939
Phocaeicola_vulgatus age age age -0.308 0.0973 0.00233 0.0119 abundance 1530 1290 0.00466 0.00956
Phocaeicola_vulgatus age age age 0.0112 0.0783 0.886 0.92 prevalence 1530 1290 0.00466 0.00956
Prevotella_copri_clade_B antibiotics Yes antibioticsYes -8.34 2.51 0.0024 0.0121 abundance 1530 40 0.00479 0.00982
Prevotella_copri_clade_B antibiotics Yes antibioticsYes -1.29 0.889 0.146 0.216 prevalence 1530 40 0.00479 0.00982
Lacrimispora_celerecrescens antibiotics Yes antibioticsYes 0.809 0.29 0.00244 0.0122 abundance 1530 756 0.00488 0.00998
Lacrimispora_celerecrescens antibiotics Yes antibioticsYes 0.05 0.191 0.793 0.842 prevalence 1530 756 0.00488 0.00998
Proteus_mirabilis age age age 0.275 0.551 1 1 abundance 1530 100 0.00494 0.0101
Proteus_mirabilis age age age -0.382 0.126 0.00247 0.00602 prevalence 1530 100 0.00494 0.0101
Bacteroides_salyersiae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -4.07 1.25 0.0025 0.0123 abundance 1530 150 0.00498 0.0102
Bacteroides_salyersiae dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.5 0.526 0.00434 0.00995 prevalence 1530 150 0.00498 0.0102
Akkermansia_sp_KLE1798 age age age -0.397 0.142 0.0051 0.0115 prevalence 1530 70 0.0051 0.0104
Bacteroides_eggerthii diagnosis UC diagnosisUC 0.278 0.587 1 1 abundance 1530 409 0.00515 0.0105
Bacteroides_eggerthii diagnosis UC diagnosisUC -0.467 0.155 0.00258 0.00627 prevalence 1530 409 0.00515 0.0105
Bacteroides_ovatus antibiotics Yes antibioticsYes 0.712 0.26 0.00264 0.013 abundance 1530 1180 0.00527 0.0107
Bacteroides_ovatus antibiotics Yes antibioticsYes 0.226 0.226 0.317 0.415 prevalence 1530 1180 0.00527 0.0107
Waltera_intestinalis reads reads reads -0.629 0.152 0.0597 0.156 abundance 1530 524 0.00558 0.0113
Waltera_intestinalis reads reads reads 0.175 0.0586 0.0028 0.00676 prevalence 1530 524 0.00558 0.0113
Collinsella_SGB14861 age age age -0.297 0.0956 0.00284 0.0139 abundance 1530 593 0.00568 0.0115
GGB9453_SGB14844 diagnosis UC diagnosisUC -1.29 0.45 0.00285 0.0139 abundance 1530 222 0.00569 0.0115
Collinsella_SGB14861 age age age 0.0721 0.0552 0.191 0.273 prevalence 1530 593 0.00568 0.0115
GGB9453_SGB14844 diagnosis UC diagnosisUC 0.202 0.193 0.296 0.391 prevalence 1530 222 0.00569 0.0115
Phascolarctobacterium_faecium dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.504 1.35 0.502 0.785 abundance 1530 503 0.0058 0.0117
Phascolarctobacterium_faecium dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.8 0.606 0.0029 0.00699 prevalence 1530 503 0.0058 0.0117
Ruminococcus_torques diagnosis UC diagnosisUC 0.575 0.197 0.011 0.0412 abundance 1530 1090 0.0059 0.0118
Ruminococcus_torques diagnosis UC diagnosisUC -0.519 0.175 0.00296 0.00709 prevalence 1530 1090 0.0059 0.0118
Paraprevotella_clara age age age -0.889 0.293 0.00315 0.0151 abundance 1530 178 0.00629 0.0126
Paraprevotella_clara age age age -0.187 0.0866 0.031 0.0578 prevalence 1530 178 0.00629 0.0126
Alistipes_communis diagnosis CD diagnosisCD -0.831 0.257 0.00323 0.0153 abundance 1530 407 0.00645 0.0129
Alistipes_communis diagnosis CD diagnosisCD 0.133 0.143 0.355 0.453 prevalence 1530 407 0.00645 0.0129
Parabacteroides_merdae diagnosis UC diagnosisUC -0.516 0.199 0.00324 0.0153 abundance 1530 826 0.00648 0.0129
Parabacteroides_merdae diagnosis UC diagnosisUC 0.301 0.146 0.04 0.0715 prevalence 1530 826 0.00648 0.0129
Waltera_intestinalis antibiotics Yes antibioticsYes 0.296 0.624 0.555 0.855 abundance 1530 524 0.0065 0.0129
Waltera_intestinalis antibiotics Yes antibioticsYes -0.672 0.228 0.00325 0.00776 prevalence 1530 524 0.0065 0.0129
Phocaeicola_coprocola age age age 0.232 0.382 1 1 abundance 1530 101 0.00652 0.013
Phocaeicola_coprocola age age age 0.288 0.098 0.00327 0.00777 prevalence 1530 101 0.00652 0.013
Alistipes_finegoldii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 4.82 2.51 0.0791 0.192 abundance 1530 639 0.00663 0.0131
Alistipes_finegoldii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.86 0.974 0.00332 0.00789 prevalence 1530 639 0.00663 0.0131
Prevotella_marseillensis diagnosis UC diagnosisUC 2.13 0.785 0.00666 0.0147 prevalence 1530 18 0.00666 0.0132
Eisenbergiella_massiliensis reads reads reads -0.6 0.156 0.0994 0.232 abundance 1530 417 0.00686 0.0135
Eisenbergiella_massiliensis reads reads reads 0.173 0.0591 0.00343 0.00812 prevalence 1530 417 0.00686 0.0135
Phocaeicola_sartorii antibiotics Yes antibioticsYes -0.117 0.446 1 1 abundance 1530 424 0.00705 0.0139
Ruminococcus_lactaris dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.0151 2.41 0.862 1 abundance 1530 379 0.00706 0.0139
Phocaeicola_sartorii antibiotics Yes antibioticsYes 0.615 0.211 0.00353 0.00832 prevalence 1530 424 0.00705 0.0139
Ruminococcus_lactaris dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.84 0.975 0.00353 0.00832 prevalence 1530 379 0.00706 0.0139
Firmicutes_bacterium_AF16_15 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.16 0.986 0.113 0.256 abundance 1530 827 0.00707 0.0139
Firmicutes_bacterium_AF16_15 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.26 0.433 0.00354 0.00832 prevalence 1530 827 0.00707 0.0139
Bacteroides_finegoldii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -9.3 3.32 0.00375 0.0174 abundance 1530 333 0.00748 0.0147
Bacteroides_finegoldii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.53 0.977 0.00968 0.0207 prevalence 1530 333 0.00748 0.0147
Clostridiaceae_bacterium antibiotics Yes antibioticsYes -0.0144 0.254 1 1 abundance 1530 1110 0.00763 0.0149
Clostridiaceae_bacterium antibiotics Yes antibioticsYes -0.568 0.196 0.00382 0.00893 prevalence 1530 1110 0.00763 0.0149
Ruminococcus_torques antibiotics Yes antibioticsYes 0.175 0.248 1 1 abundance 1530 1090 0.00768 0.015
Ruminococcus_torques antibiotics Yes antibioticsYes 0.619 0.214 0.00385 0.00897 prevalence 1530 1090 0.00768 0.015
Dorea_longicatena diagnosis CD diagnosisCD 0.41 0.165 0.00388 0.0178 abundance 1530 1020 0.00775 0.0151
Dorea_longicatena diagnosis CD diagnosisCD -0.0966 0.149 0.517 0.613 prevalence 1530 1020 0.00775 0.0151
Gemmiger_formicilis age age age -0.394 0.132 0.00394 0.018 abundance 1530 472 0.00787 0.0153
Gemmiger_formicilis age age age -0.132 0.0601 0.0286 0.0537 prevalence 1530 472 0.00787 0.0153
Clostridium_sp_AM49_4BH dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.341 1.82 0.759 1 abundance 1530 344 0.00795 0.0154
Clostridium_sp_AM49_4BH dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.97 0.684 0.00398 0.00927 prevalence 1530 344 0.00795 0.0154
GGB3278_SGB4328 antibiotics Yes antibioticsYes 0.0294 1.56 1 1 abundance 1530 179 0.00831 0.0161
GGB3278_SGB4328 antibiotics Yes antibioticsYes -1.61 0.564 0.00416 0.00965 prevalence 1530 179 0.00831 0.0161
Proteus_mirabilis antibiotics Yes antibioticsYes 2.78 0.972 0.00417 0.0189 abundance 1530 100 0.00833 0.0161
Proteus_mirabilis antibiotics Yes antibioticsYes -0.0304 0.342 0.929 0.951 prevalence 1530 100 0.00833 0.0161
Lacrimispora_amygdalina antibiotics Yes antibioticsYes -0.37 0.298 0.318 0.555 abundance 1530 865 0.00855 0.0165
Lacrimispora_amygdalina antibiotics Yes antibioticsYes -0.554 0.194 0.00428 0.0099 prevalence 1530 865 0.00855 0.0165
Eubacterium_ventriosum reads reads reads -0.305 0.117 1 1 abundance 1530 520 0.00859 0.0166
GGB16040_SGB9347 reads reads reads -0.224 0.242 1 1 abundance 1530 114 0.0086 0.0166
Eubacterium_ventriosum reads reads reads 0.165 0.0577 0.00431 0.00992 prevalence 1530 520 0.00859 0.0166
GGB16040_SGB9347 reads reads reads 0.288 0.101 0.00431 0.00992 prevalence 1530 114 0.0086 0.0166
Coprococcus_eutactus antibiotics Yes antibioticsYes -2.98 1.01 0.00432 0.0194 abundance 1530 177 0.00862 0.0166
Coprococcus_eutactus antibiotics Yes antibioticsYes -0.664 0.403 0.0993 0.156 prevalence 1530 177 0.00862 0.0166
Bifidobacterium_longum diagnosis CD diagnosisCD 0.607 0.237 0.00441 0.0196 abundance 1530 843 0.0088 0.0169
Bifidobacterium_longum diagnosis CD diagnosisCD -0.298 0.14 0.0336 0.0618 prevalence 1530 843 0.0088 0.0169
GGB9453_SGB14844 reads reads reads -0.928 0.204 0.00443 0.0196 abundance 1530 222 0.00883 0.0169
GGB9453_SGB14844 reads reads reads 0.00265 0.0748 0.972 0.979 prevalence 1530 222 0.00883 0.0169
GGB3277_SGB4327 diagnosis UC diagnosisUC 1.55 0.51 0.00446 0.0197 abundance 1530 152 0.00889 0.017
GGB3277_SGB4327 diagnosis UC diagnosisUC 0.152 0.225 0.5 0.599 prevalence 1530 152 0.00889 0.017
Prevotella_sp_885 antibiotics Yes antibioticsYes -4.39 1.46 0.0045 0.0198 abundance 1530 69 0.00898 0.0171
Prevotella_sp_885 antibiotics Yes antibioticsYes -0.0491 0.396 0.901 0.931 prevalence 1530 69 0.00898 0.0171
Roseburia_faecis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.0606 0.852 0.586 0.894 abundance 1530 922 0.00942 0.0179
Roseburia_faecis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.05 0.372 0.00472 0.0108 prevalence 1530 922 0.00942 0.0179
Bacteroides_faecis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 5.21 1.7 0.00485 0.021 abundance 1530 434 0.00967 0.0184
Bacteroides_faecis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.767 0.5 0.125 0.191 prevalence 1530 434 0.00967 0.0184
Ruminococcus_gnavus reads reads reads -0.599 0.101 0.0107 0.0405 abundance 1530 767 0.00978 0.0186
Ruminococcus_gnavus reads reads reads 0.153 0.0544 0.0049 0.0112 prevalence 1530 767 0.00978 0.0186
GGB1680_SGB2312 diagnosis UC diagnosisUC -2.93 1.14 0.00993 0.021 prevalence 1530 12 0.00993 0.0188
GGB3175_SGB4191 age age age -0.118 0.264 1 1 abundance 1530 154 0.00996 0.0188
GGB3175_SGB4191 age age age 0.227 0.0809 0.00499 0.0113 prevalence 1530 154 0.00996 0.0188
Eubacterium_siraeum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.21 1.92 0.174 0.355 abundance 1530 565 0.01 0.0189
Eubacterium_siraeum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.69 0.603 0.00502 0.0114 prevalence 1530 565 0.01 0.0189
Escherichia_coli dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.719 0.619 0.61 0.922 abundance 1530 707 0.0101 0.019
Escherichia_coli dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.984 0.351 0.00505 0.0114 prevalence 1530 707 0.0101 0.019
Paraprevotella_clara reads reads reads 0.189 0.24 0.028 0.0844 abundance 1530 178 0.0102 0.0193
Paraprevotella_clara reads reads reads 0.223 0.0799 0.00514 0.0116 prevalence 1530 178 0.0102 0.0193
Flavonifractor_plautii antibiotics Yes antibioticsYes 0.606 0.242 0.00517 0.0222 abundance 1530 1220 0.0103 0.0194
Flavonifractor_plautii antibiotics Yes antibioticsYes -0.239 0.216 0.268 0.36 prevalence 1530 1220 0.0103 0.0194
Clostridiales_bacterium diagnosis CD diagnosisCD 0.23 0.179 0.096 0.224 abundance 1530 985 0.0105 0.0198
Clostridiales_bacterium diagnosis CD diagnosisCD -0.433 0.155 0.00529 0.0119 prevalence 1530 985 0.0105 0.0198
GGB3278_SGB4328 reads reads reads -0.101 0.238 1 1 abundance 1530 179 0.0106 0.0199
GGB3278_SGB4328 reads reads reads 0.229 0.0823 0.00532 0.0119 prevalence 1530 179 0.0106 0.0199
Dialister_invisus reads reads reads -0.31 0.088 1 1 abundance 1530 726 0.0106 0.0199
Dialister_invisus reads reads reads 0.153 0.0551 0.00533 0.0119 prevalence 1530 726 0.0106 0.0199
GGB781_SGB1024 diagnosis CD diagnosisCD 1.99 0.782 0.0111 0.0233 prevalence 1530 18 0.0111 0.0207
Clostridium_sp_1001270H_150608_G6 age age age 0.594 0.298 0.044 0.12 abundance 1530 141 0.0112 0.0208
GGB3304_SGB4367 diagnosis CD diagnosisCD 0.17 0.505 1 1 abundance 1530 155 0.0112 0.0208
Clostridium_sp_1001270H_150608_G6 age age age 0.232 0.0836 0.00562 0.0125 prevalence 1530 141 0.0112 0.0208
GGB3304_SGB4367 diagnosis CD diagnosisCD -0.607 0.219 0.00562 0.0125 prevalence 1530 155 0.0112 0.0208
Lachnospira_sp_NSJ_43 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.11 1.85 0.119 0.267 abundance 1530 296 0.0117 0.0216
Lachnospira_sp_NSJ_43 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.9 0.688 0.00585 0.013 prevalence 1530 296 0.0117 0.0216
Bacteroides_fragilis age age age -0.0491 0.113 1 1 abundance 1530 787 0.012 0.0223
Bacteroides_fragilis age age age -0.147 0.0535 0.00603 0.0134 prevalence 1530 787 0.012 0.0223
Eubacterium_siraeum reads reads reads -0.755 0.15 0.0061 0.0256 abundance 1530 565 0.0122 0.0225
Eubacterium_siraeum reads reads reads 0.154 0.058 0.00774 0.0168 prevalence 1530 565 0.0122 0.0225
GGB9713_SGB15249 reads reads reads 0.129 0.171 0.0063 0.0264 abundance 1530 329 0.0126 0.0232
GGB9713_SGB15249 reads reads reads 0.143 0.0683 0.0368 0.0666 prevalence 1530 329 0.0126 0.0232
Blautia_faecis diagnosis CD diagnosisCD 0.406 0.175 0.0068 0.0283 abundance 1530 1120 0.0136 0.025
Blautia_faecis diagnosis CD diagnosisCD 0.0798 0.161 0.621 0.705 prevalence 1530 1120 0.0136 0.025
Alistipes_SGB2313 diagnosis UC diagnosisUC -2.2 0.817 0.00705 0.029 abundance 1530 73 0.0141 0.0258
Alistipes_SGB2313 diagnosis UC diagnosisUC -0.588 0.31 0.0576 0.0982 prevalence 1530 73 0.0141 0.0258
Tyzzerella_nexilis antibiotics Yes antibioticsYes 1.7 0.841 0.0369 0.105 abundance 1530 188 0.0141 0.026
Tyzzerella_nexilis antibiotics Yes antibioticsYes -0.918 0.341 0.0071 0.0157 prevalence 1530 188 0.0141 0.026
Haemophilus_parainfluenzae reads reads reads -0.63 0.107 0.0072 0.0293 abundance 1530 674 0.0144 0.0263
Haemophilus_parainfluenzae reads reads reads 0.0457 0.0545 0.401 0.501 prevalence 1530 674 0.0144 0.0263
Eubacterium_ventriosum diagnosis UC diagnosisUC 0.0724 0.274 1 1 abundance 1530 520 0.0145 0.0264
Eubacterium_ventriosum diagnosis UC diagnosisUC -0.39 0.145 0.00726 0.016 prevalence 1530 520 0.0145 0.0264
Rikenellaceae_bacterium diagnosis UC diagnosisUC -0.747 0.307 0.0149 0.0299 prevalence 1530 67 0.0149 0.0271
Ruminococcus_gnavus antibiotics Yes antibioticsYes -0.137 0.304 1 1 abundance 1530 767 0.0152 0.0277
Ruminococcus_gnavus antibiotics Yes antibioticsYes 0.491 0.184 0.00763 0.0167 prevalence 1530 767 0.0152 0.0277
Bacteroides_caccae age age age -0.0856 0.0698 1 1 abundance 1530 958 0.0154 0.028
Proteus_mirabilis diagnosis UC diagnosisUC -1.02 1.02 0.288 0.51 abundance 1530 100 0.0154 0.028
Roseburia_hominis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.46 0.791 0.183 0.372 abundance 1530 876 0.0154 0.028
Bacteroides_caccae age age age 0.154 0.058 0.00774 0.0168 prevalence 1530 958 0.0154 0.028
Proteus_mirabilis diagnosis UC diagnosisUC -0.863 0.324 0.00775 0.0168 prevalence 1530 100 0.0154 0.028
Roseburia_hominis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.998 0.375 0.00772 0.0168 prevalence 1530 876 0.0154 0.028
GGB1680_SGB2312 diagnosis CD diagnosisCD -1.87 0.777 0.0159 0.0318 prevalence 1530 12 0.0159 0.0287
Eisenbergiella_massiliensis diagnosis UC diagnosisUC 0.447 0.445 0.4 0.654 abundance 1530 417 0.016 0.0289
Eisenbergiella_massiliensis diagnosis UC diagnosisUC 0.44 0.166 0.00802 0.0174 prevalence 1530 417 0.016 0.0289
Ruminococcus_sp_BSD2780120874_150323_B10 antibiotics Yes antibioticsYes -2.11 0.876 0.0163 0.0325 prevalence 1530 90 0.0163 0.0293
Bacteroides_eggerthii age age age 0.579 0.222 0.0082 0.0329 abundance 1530 409 0.0163 0.0294
Bacteroides_eggerthii age age age 0.00796 0.0612 0.896 0.927 prevalence 1530 409 0.0163 0.0294
Coprococcus_eutactus reads reads reads 0.246 0.22 0.00822 0.0329 abundance 1530 177 0.0164 0.0294
Coprococcus_eutactus reads reads reads 0.0223 0.0883 0.801 0.846 prevalence 1530 177 0.0164 0.0294
Clostridium_leptum diagnosis UC diagnosisUC -0.118 0.257 1 1 abundance 1530 652 0.0168 0.0301
GGB51647_SGB4348 age age age -0.914 0.337 0.00843 0.0334 abundance 1530 123 0.0168 0.0301
Clostridium_leptum diagnosis UC diagnosisUC -0.383 0.146 0.00844 0.0182 prevalence 1530 652 0.0168 0.0301
GGB51647_SGB4348 age age age -0.174 0.1 0.0832 0.133 prevalence 1530 123 0.0168 0.0301
GGB1543_SGB2126 diagnosis CD diagnosisCD -5.68 2.03 0.00887 0.0347 abundance 1530 42 0.0177 0.0316
GGB1543_SGB2126 diagnosis CD diagnosisCD -0.898 0.417 0.0313 0.0583 prevalence 1530 42 0.0177 0.0316
GGB1549_SGB2133 diagnosis UC diagnosisUC -1.23 1.13 0.256 0.466 abundance 1530 46 0.0178 0.0317
GGB1549_SGB2133 diagnosis UC diagnosisUC -1.15 0.439 0.00892 0.0192 prevalence 1530 46 0.0178 0.0317
Coprococcus_comes age age age -0.213 0.0816 1 1 abundance 1530 759 0.0179 0.0319
Coprococcus_comes age age age -0.142 0.0545 0.00897 0.0193 prevalence 1530 759 0.0179 0.0319
Hungatella_hathewayi reads reads reads -0.751 0.156 0.00901 0.0351 abundance 1530 451 0.0179 0.0319
Hungatella_hathewayi reads reads reads 0.117 0.057 0.0406 0.0724 prevalence 1530 451 0.0179 0.0319
Klebsiella_pneumoniae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 4.27 1.46 0.00915 0.0355 abundance 1530 119 0.0182 0.0324
Klebsiella_pneumoniae dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1 0.531 0.0597 0.101 prevalence 1530 119 0.0182 0.0324
GGB9480_SGB14874 reads reads reads -0.331 0.125 1 1 abundance 1530 332 0.0188 0.0334
GGB9480_SGB14874 reads reads reads 0.17 0.0654 0.00945 0.0203 prevalence 1530 332 0.0188 0.0334
Alistipes_dispar dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 2.47 1.01 0.0095 0.0366 abundance 1530 83 0.0189 0.0335
Alistipes_dispar dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.745 0.361 0.039 0.07 prevalence 1530 83 0.0189 0.0335
Lachnospira_eligens diagnosis UC diagnosisUC 0.644 0.22 0.00968 0.037 abundance 1530 929 0.0193 0.0341
Lachnospira_eligens diagnosis UC diagnosisUC 0.114 0.159 0.474 0.574 prevalence 1530 929 0.0193 0.0341
Eisenbergiella_massiliensis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 2.65 0.863 0.0097 0.037 abundance 1530 417 0.0193 0.0341
Eisenbergiella_massiliensis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.261 0.347 0.453 0.556 prevalence 1530 417 0.0193 0.0341
Rikenellaceae_bacterium age age age 0.26 0.111 0.0193 0.0379 prevalence 1530 67 0.0193 0.0341
Bacteroides_intestinalis diagnosis CD diagnosisCD -1.61 0.642 0.0179 0.0598 abundance 1530 158 0.0194 0.0341
Bacteroides_intestinalis diagnosis CD diagnosisCD 0.575 0.223 0.00975 0.0209 prevalence 1530 158 0.0194 0.0341
GGB16040_SGB9347 diagnosis CD diagnosisCD 0.421 0.795 0.539 0.832 abundance 1530 114 0.0195 0.0342
GGB16040_SGB9347 diagnosis CD diagnosisCD 0.754 0.292 0.00978 0.0209 prevalence 1530 114 0.0195 0.0342
Bacteroides_uniformis diagnosis UC diagnosisUC 0.286 0.186 1 1 abundance 1530 1240 0.0195 0.0342
Bacteroides_uniformis diagnosis UC diagnosisUC 0.515 0.199 0.0098 0.0209 prevalence 1530 1240 0.0195 0.0342
Faecalibacterium_SGB15315 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.835 1.17 0.291 0.514 abundance 1530 619 0.0197 0.0344
Faecalibacterium_SGB15315 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.12 0.432 0.00988 0.021 prevalence 1530 619 0.0197 0.0344
Bifidobacterium_longum antibiotics Yes antibioticsYes 0.773 0.361 0.0196 0.0641 abundance 1530 843 0.0198 0.0346
Bifidobacterium_longum antibiotics Yes antibioticsYes -0.481 0.187 0.00996 0.021 prevalence 1530 843 0.0198 0.0346
Blautia_faecis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.871 0.483 0.334 0.577 abundance 1530 1120 0.0199 0.0347
Blautia_faecis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.908 0.353 0.01 0.0211 prevalence 1530 1120 0.0199 0.0347
Clostridium_symbiosum antibiotics Yes antibioticsYes 0.892 0.375 0.0103 0.0391 abundance 1530 539 0.0205 0.0357
Clostridium_symbiosum antibiotics Yes antibioticsYes 0.425 0.183 0.02 0.0388 prevalence 1530 539 0.0205 0.0357
Sutterella_wadsworthensis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.14 0.946 0.438 0.702 abundance 1530 536 0.0213 0.0371
Sutterella_wadsworthensis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.36 0.533 0.0107 0.0225 prevalence 1530 536 0.0213 0.0371
Ruminococcus_lactaris age age age -0.376 0.143 0.011 0.0412 abundance 1530 379 0.0219 0.038
Ruminococcus_lactaris age age age 0.109 0.0599 0.0694 0.114 prevalence 1530 379 0.0219 0.038
Roseburia_inulinivorans age age age -0.104 0.0816 1 1 abundance 1530 951 0.0222 0.0384
Roseburia_inulinivorans age age age -0.146 0.0576 0.0111 0.0233 prevalence 1530 951 0.0222 0.0384
GGB3175_SGB4191 reads reads reads 0.403 0.29 0.0114 0.042 abundance 1530 154 0.0227 0.0392
GGB3175_SGB4191 reads reads reads 0.171 0.0893 0.0558 0.0961 prevalence 1530 154 0.0227 0.0392
Roseburia_intestinalis reads reads reads -0.317 0.118 1 1 abundance 1530 842 0.0227 0.0392
Roseburia_intestinalis reads reads reads 0.138 0.0546 0.0114 0.0238 prevalence 1530 842 0.0227 0.0392
GGB4237_SGB5728 reads reads reads 0.576 0.253 0.0228 0.0441 prevalence 1530 6 0.0228 0.0394
Bacteroides_cellulosilyticus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 4.22 1.51 0.0116 0.0426 abundance 1530 433 0.0231 0.0397
Bacteroides_cellulosilyticus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.19 0.536 0.0262 0.0496 prevalence 1530 433 0.0231 0.0397
Phocaeicola_dorei diagnosis UC diagnosisUC -0.192 0.506 0.601 0.91 abundance 1530 769 0.0235 0.0403
Phocaeicola_dorei diagnosis UC diagnosisUC 0.383 0.152 0.0118 0.0246 prevalence 1530 769 0.0235 0.0403
Prevotella_stercorea diagnosis CD diagnosisCD 1.73 0.772 0.025 0.0479 prevalence 1530 40 0.025 0.0429
Blautia_wexlerae antibiotics Yes antibioticsYes 0.53 0.243 0.0132 0.0476 abundance 1530 1300 0.0262 0.0448
GGB3175_SGB4191 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.695 2.15 0.672 1 abundance 1530 154 0.0262 0.0448
Blautia_wexlerae antibiotics Yes antibioticsYes -0.499 0.226 0.0275 0.052 prevalence 1530 1300 0.0262 0.0448
GGB3175_SGB4191 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.71 0.688 0.0132 0.0273 prevalence 1530 154 0.0262 0.0448
Veillonella_dispar antibiotics Yes antibioticsYes 0.351 0.527 0.422 0.685 abundance 1530 526 0.0266 0.0454
Veillonella_dispar antibiotics Yes antibioticsYes -0.519 0.21 0.0134 0.0276 prevalence 1530 526 0.0266 0.0454
GGB16040_SGB9347 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.877 1.99 0.741 1 abundance 1530 114 0.027 0.0459
Hungatella_hathewayi diagnosis UC diagnosisUC -0.954 0.414 0.0136 0.0486 abundance 1530 451 0.0269 0.0459
Phocaeicola_vulgatus diagnosis UC diagnosisUC 0.405 0.261 0.203 0.397 abundance 1530 1290 0.027 0.0459
GGB16040_SGB9347 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -1.75 0.71 0.0136 0.0279 prevalence 1530 114 0.027 0.0459
Hungatella_hathewayi diagnosis UC diagnosisUC 0.245 0.157 0.12 0.183 prevalence 1530 451 0.0269 0.0459
Phocaeicola_vulgatus diagnosis UC diagnosisUC 0.602 0.244 0.0136 0.0279 prevalence 1530 1290 0.027 0.0459
Oscillibacter_sp_ER4 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.73 1.5 0.0376 0.107 abundance 1530 458 0.0272 0.0462
Oscillibacter_sp_ER4 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.77 0.72 0.0137 0.0281 prevalence 1530 458 0.0272 0.0462
Eubacterium_ventriosum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.674 0.962 0.263 0.474 abundance 1530 520 0.0275 0.0466
Eubacterium_ventriosum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.05 0.426 0.0138 0.0284 prevalence 1530 520 0.0275 0.0466
Ruthenibacterium_lactatiformans antibiotics Yes antibioticsYes -0.178 0.323 1 1 abundance 1530 797 0.0276 0.0466
Ruthenibacterium_lactatiformans antibiotics Yes antibioticsYes 0.465 0.189 0.0139 0.0284 prevalence 1530 797 0.0276 0.0466
Coprococcus_comes antibiotics Yes antibioticsYes 0.486 0.266 0.0362 0.104 abundance 1530 759 0.0278 0.047
Coprococcus_comes antibiotics Yes antibioticsYes 0.482 0.196 0.014 0.0286 prevalence 1530 759 0.0278 0.047
Akkermansia_muciniphila diagnosis CD diagnosisCD -0.868 0.364 0.0289 0.0864 abundance 1530 407 0.0279 0.047
Akkermansia_muciniphila diagnosis CD diagnosisCD -0.357 0.145 0.014 0.0286 prevalence 1530 407 0.0279 0.047
Alistipes_finegoldii diagnosis CD diagnosisCD -0.0369 0.229 1 1 abundance 1530 639 0.0282 0.0473
Barnesiella_intestinihominis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.44 1.78 0.112 0.254 abundance 1530 431 0.0282 0.0473
Fusicatenibacter_saccharivorans diagnosis CD diagnosisCD 0.324 0.16 0.0142 0.0503 abundance 1530 1120 0.0282 0.0473
Alistipes_finegoldii diagnosis CD diagnosisCD -0.326 0.133 0.0142 0.0288 prevalence 1530 639 0.0282 0.0473
Barnesiella_intestinihominis dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.77 0.72 0.0142 0.0288 prevalence 1530 431 0.0282 0.0473
Fusicatenibacter_saccharivorans diagnosis CD diagnosisCD -0.253 0.184 0.169 0.246 prevalence 1530 1120 0.0282 0.0473
Roseburia_sp_AF02_12 antibiotics Yes antibioticsYes -1.5 0.755 0.0597 0.156 abundance 1530 363 0.0291 0.0487
Roseburia_sp_AF02_12 antibiotics Yes antibioticsYes -0.687 0.281 0.0146 0.0297 prevalence 1530 363 0.0291 0.0487
Bacteroides_eggerthii antibiotics Yes antibioticsYes -0.802 0.793 0.358 0.6 abundance 1530 409 0.0293 0.0491
Bacteroides_eggerthii antibiotics Yes antibioticsYes 0.534 0.219 0.0148 0.0299 prevalence 1530 409 0.0293 0.0491
Faecalibacterium_SGB15346 antibiotics Yes antibioticsYes -0.0726 0.382 1 1 abundance 1530 743 0.0295 0.0492
Faecalibacterium_SGB15346 antibiotics Yes antibioticsYes -0.471 0.194 0.0149 0.0299 prevalence 1530 743 0.0295 0.0492
Eubacterium_ventriosum age age age -0.274 0.108 0.015 0.0527 abundance 1530 520 0.0298 0.0496
Eubacterium_ventriosum age age age 0.0568 0.056 0.31 0.407 prevalence 1530 520 0.0298 0.0496
Ruminococcus_gnavus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.72 0.538 0.0151 0.0527 abundance 1530 767 0.0299 0.0497
Ruminococcus_gnavus dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.721 0.351 0.04 0.0715 prevalence 1530 767 0.0299 0.0497
Phocaeicola_massiliensis age age age -0.244 0.137 0.089 0.212 abundance 1530 396 0.0312 0.0519
Phocaeicola_massiliensis age age age 0.141 0.0582 0.0157 0.0316 prevalence 1530 396 0.0312 0.0519
Roseburia_sp_AF02_12 age age age 0.327 0.139 0.0159 0.0546 abundance 1530 363 0.0316 0.0525
Roseburia_sp_AF02_12 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -2.83 1.08 0.016 0.0546 abundance 1530 363 0.0317 0.0525
Roseburia_sp_AF02_12 age age age 0.0663 0.0623 0.288 0.384 prevalence 1530 363 0.0316 0.0525
Roseburia_sp_AF02_12 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.82 0.382 0.0319 0.0594 prevalence 1530 363 0.0317 0.0525
Oscillibacter_sp_ER4 diagnosis CD diagnosisCD 0.339 0.24 0.0903 0.214 abundance 1530 458 0.0321 0.0531
Oscillibacter_sp_ER4 diagnosis CD diagnosisCD -0.336 0.14 0.0162 0.0324 prevalence 1530 458 0.0321 0.0531
Ruminococcus_bromii reads reads reads -0.352 0.125 1 1 abundance 1530 429 0.0323 0.0534
Ruminococcus_bromii reads reads reads 0.147 0.0614 0.0163 0.0325 prevalence 1530 429 0.0323 0.0534
Alistipes_dispar diagnosis CD diagnosisCD -1.48 0.576 0.0165 0.0557 abundance 1530 83 0.0327 0.0537
Collinsella_SGB14861 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.571 1.23 0.428 0.691 abundance 1530 593 0.0327 0.0537
Ruthenibacterium_lactatiformans diagnosis UC diagnosisUC -0.544 0.256 0.0164 0.0557 abundance 1530 797 0.0326 0.0537
Alistipes_dispar diagnosis CD diagnosisCD -0.429 0.283 0.13 0.198 prevalence 1530 83 0.0327 0.0537
Collinsella_SGB14861 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.28 0.533 0.0165 0.0328 prevalence 1530 593 0.0327 0.0537
Ruthenibacterium_lactatiformans diagnosis UC diagnosisUC -0.0819 0.147 0.578 0.667 prevalence 1530 797 0.0326 0.0537
Prevotella_copri_clade_E diagnosis CD diagnosisCD 1.65 0.776 0.0329 0.061 prevalence 1530 38 0.0329 0.054
Prevotella_copri_clade_C diagnosis CD diagnosisCD 2.3 1.08 0.033 0.0611 prevalence 1530 16 0.033 0.0541
Bacteroides_ilei antibiotics Yes antibioticsYes 1.13 0.532 0.0331 0.0611 prevalence 1530 17 0.0331 0.0541
Lachnospira_pectinoschiza diagnosis UC diagnosisUC 0.77 0.291 0.0167 0.0563 abundance 1530 500 0.0331 0.0541
Lachnospira_pectinoschiza diagnosis UC diagnosisUC -0.183 0.148 0.217 0.302 prevalence 1530 500 0.0331 0.0541
Faecalibacterium_SGB15346 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.637 0.784 0.185 0.373 abundance 1530 743 0.0333 0.0543
Faecalibacterium_SGB15346 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.866 0.362 0.0168 0.0334 prevalence 1530 743 0.0333 0.0543
Bacteroides_eggerthii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -2.82 2.36 0.173 0.355 abundance 1530 409 0.0334 0.0544
Bacteroides_eggerthii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.29 0.54 0.0168 0.0334 prevalence 1530 409 0.0334 0.0544
Clostridium_sp_AF36_4 reads reads reads -0.0934 0.103 1 1 abundance 1530 568 0.035 0.057
Clostridium_sp_AF36_4 reads reads reads 0.137 0.0578 0.0177 0.035 prevalence 1530 568 0.035 0.057
Bacteroides_cellulosilyticus reads reads reads -0.281 0.149 1 1 abundance 1530 433 0.0358 0.0581
Eubacterium_rectale diagnosis CD diagnosisCD -0.458 0.165 0.0181 0.0598 abundance 1530 1210 0.0358 0.0581
Bacteroides_cellulosilyticus reads reads reads 0.144 0.0609 0.0181 0.0357 prevalence 1530 433 0.0358 0.0581
Eubacterium_rectale diagnosis CD diagnosisCD -0.0705 0.195 0.718 0.784 prevalence 1530 1210 0.0358 0.0581
Oscillospiraceae_bacterium reads reads reads -0.283 0.287 1 1 abundance 1530 81 0.0364 0.0588
Oscillospiraceae_bacterium reads reads reads 0.274 0.116 0.0183 0.0362 prevalence 1530 81 0.0364 0.0588
Faecalibacterium_SGB15346 age age age -0.0229 0.0994 1 1 abundance 1530 743 0.0365 0.059
Faecalibacterium_SGB15346 age age age 0.129 0.0546 0.0184 0.0363 prevalence 1530 743 0.0365 0.059
Clostridiaceae_bacterium_Marseille_Q4149 reads reads reads -0.376 0.232 1 1 abundance 1530 181 0.0389 0.0627
Clostridium_sp_AF36_4 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.212 0.886 0.487 0.765 abundance 1530 568 0.0389 0.0627
Clostridiaceae_bacterium_Marseille_Q4149 reads reads reads 0.187 0.0802 0.0197 0.0384 prevalence 1530 181 0.0389 0.0627
Clostridium_sp_AF36_4 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.06 0.455 0.0196 0.0384 prevalence 1530 568 0.0389 0.0627
Bacteroides_caccae diagnosis UC diagnosisUC 0.103 0.188 1 1 abundance 1530 958 0.0394 0.0634
Bacteroides_caccae diagnosis UC diagnosisUC -0.358 0.154 0.0199 0.0388 prevalence 1530 958 0.0394 0.0634
Tyzzerella_nexilis reads reads reads -0.785 0.19 0.0205 0.0668 abundance 1530 188 0.0406 0.0651
Tyzzerella_nexilis reads reads reads 0.00685 0.0803 0.932 0.952 prevalence 1530 188 0.0406 0.0651
Phascolarctobacterium_succinatutens age age age -0.328 0.135 0.0207 0.0671 abundance 1530 125 0.0409 0.0656
Phascolarctobacterium_succinatutens age age age 0.036 0.09 0.689 0.761 prevalence 1530 125 0.0409 0.0656
Clostridium_sp_AM22_11AC diagnosis UC diagnosisUC 0.621 0.237 0.0208 0.0675 abundance 1530 730 0.0413 0.0661
Clostridium_sp_AM22_11AC diagnosis UC diagnosisUC -0.102 0.145 0.483 0.582 prevalence 1530 730 0.0413 0.0661
Prevotella_SGB48271 diagnosis UC diagnosisUC 2.27 1.12 0.0422 0.075 prevalence 1530 6 0.0422 0.0675
Dysgonomonas_mossii reads reads reads -0.664 0.667 0.633 0.954 abundance 1530 31 0.0431 0.0688
Dysgonomonas_mossii reads reads reads -0.467 0.203 0.0218 0.0422 prevalence 1530 31 0.0431 0.0688
Phocaeicola_sartorii age age age 0.301 0.135 0.0219 0.0701 abundance 1530 424 0.0433 0.069
Phocaeicola_sartorii age age age 0.0264 0.0637 0.679 0.754 prevalence 1530 424 0.0433 0.069
GGB9480_SGB14874 antibiotics Yes antibioticsYes -0.201 0.502 1 1 abundance 1530 332 0.0454 0.0723
GGB9480_SGB14874 antibiotics Yes antibioticsYes -0.574 0.252 0.023 0.0443 prevalence 1530 332 0.0454 0.0723
Parasutterella_SGB9260 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -0.13 0.998 0.593 0.9 abundance 1530 269 0.0456 0.0724
Parasutterella_SGB9260 dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.11 0.487 0.0231 0.0444 prevalence 1530 269 0.0456 0.0724
Ruminococcus_sp_BSD2780120874_150323_B10 reads reads reads 0.22 0.11 0.0459 0.0809 prevalence 1530 90 0.0459 0.0729
Ruminococcus_bicirculans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.48 0.537 0.194 0.384 abundance 1530 678 0.046 0.0729
Ruminococcus_bicirculans dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.541 0.238 0.0233 0.0448 prevalence 1530 678 0.046 0.0729
Faecalibacterium_SGB15346 diagnosis CD diagnosisCD -0.63 0.247 0.0237 0.0751 abundance 1530 743 0.0468 0.074
Prevotella_copri_clade_A antibiotics Yes antibioticsYes -2.67 1.14 0.0237 0.0751 abundance 1530 289 0.0468 0.074
Faecalibacterium_SGB15346 diagnosis CD diagnosisCD 0.213 0.134 0.112 0.174 prevalence 1530 743 0.0468 0.074
Prevotella_copri_clade_A antibiotics Yes antibioticsYes -0.243 0.259 0.348 0.448 prevalence 1530 289 0.0468 0.074
Dysgonomonas_mossii age age age 6.57 5.65 0.255 0.464 abundance 1530 31 0.0477 0.0752
Dysgonomonas_mossii age age age -0.5 0.222 0.0241 0.0463 prevalence 1530 31 0.0477 0.0752
Vescimonas_coprocola age age age -0.245 0.0962 1 1 abundance 1530 599 0.0497 0.0784
Vescimonas_coprocola age age age -0.128 0.0571 0.0252 0.0481 prevalence 1530 599 0.0497 0.0784
Tyzzerella_nexilis age age age -0.146 0.197 1 1 abundance 1530 188 0.0505 0.0793
Bacteroides_ilei diagnosis UC diagnosisUC 2.16 1.1 0.0505 0.0881 prevalence 1530 17 0.0505 0.0793
Tyzzerella_nexilis age age age -0.195 0.0874 0.0256 0.0488 prevalence 1530 188 0.0505 0.0793
Lachnospira_sp_NSJ_43 reads reads reads -0.736 0.176 0.0256 0.0798 abundance 1530 296 0.0506 0.0794
Lachnospira_sp_NSJ_43 reads reads reads 0.00084 0.0735 0.991 0.993 prevalence 1530 296 0.0506 0.0794
Enterocloster_bolteae antibiotics Yes antibioticsYes 0.618 0.309 0.0257 0.0798 abundance 1530 866 0.0507 0.0795
Enterocloster_bolteae antibiotics Yes antibioticsYes 0.0381 0.181 0.833 0.872 prevalence 1530 866 0.0507 0.0795
Dysosmobacter_sp_BX15 age age age 0.0536 0.0813 1 1 abundance 1530 621 0.0508 0.0795
Tyzzerella_nexilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.507 0.633 0.253 0.463 abundance 1530 188 0.0509 0.0795
Dysosmobacter_sp_BX15 age age age 0.122 0.0548 0.0257 0.049 prevalence 1530 621 0.0508 0.0795
Tyzzerella_nexilis dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD 0.612 0.275 0.0258 0.049 prevalence 1530 188 0.0509 0.0795
Dialister_invisus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.271 0.374 1 1 abundance 1530 726 0.0513 0.0798
Dialister_invisus dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -0.49 0.22 0.026 0.0493 prevalence 1530 726 0.0513 0.0798
GGB33512_SGB15201 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.75 1.93 0.0512 0.0892 prevalence 1530 121 0.0512 0.0798
Ruminococcus_gnavus diagnosis CD diagnosisCD 0.0516 0.266 1 1 abundance 1530 767 0.0531 0.0825
Ruminococcus_gnavus diagnosis CD diagnosisCD 0.299 0.135 0.0269 0.0508 prevalence 1530 767 0.0531 0.0825
GGB9342_SGB14306 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.72 1.93 0.054 0.0934 prevalence 1530 92 0.054 0.0838
Hungatella_hathewayi antibiotics Yes antibioticsYes 1.01 0.49 0.0276 0.084 abundance 1530 451 0.0544 0.0843
Hungatella_hathewayi antibiotics Yes antibioticsYes -0.12 0.194 0.536 0.629 prevalence 1530 451 0.0544 0.0843
Clostridium_sp_1001270H_150608_G6 reads reads reads 0.258 0.269 0.0276 0.084 abundance 1530 141 0.0545 0.0843
Clostridium_sp_1001270H_150608_G6 reads reads reads 0.0647 0.097 0.505 0.603 prevalence 1530 141 0.0545 0.0843
GGB9453_SGB14844 antibiotics Yes antibioticsYes -0.698 0.632 0.323 0.561 abundance 1530 222 0.0547 0.0845
Parabacteroides_distasonis antibiotics Yes antibioticsYes 0.38 0.205 0.0278 0.0842 abundance 1530 1140 0.0548 0.0845
GGB9453_SGB14844 antibiotics Yes antibioticsYes 0.509 0.231 0.0277 0.0523 prevalence 1530 222 0.0547 0.0845
Parabacteroides_distasonis antibiotics Yes antibioticsYes 0.155 0.216 0.472 0.573 prevalence 1530 1140 0.0548 0.0845
Bilophila_wadsworthia antibiotics Yes antibioticsYes 0.289 0.315 0.251 0.462 abundance 1530 764 0.056 0.0864
Bilophila_wadsworthia antibiotics Yes antibioticsYes -0.427 0.195 0.0284 0.0535 prevalence 1530 764 0.056 0.0864
Bacteroides_mediterraneensis diagnosis CD diagnosisCD -1.27 0.665 0.0564 0.097 prevalence 1530 13 0.0564 0.0868
Bacteroides_ilei diagnosis CD diagnosisCD 2.07 1.09 0.0579 0.0986 prevalence 1530 17 0.0579 0.089
Ruminococcus_bromii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.99 1.71 0.732 1 abundance 1530 429 0.0581 0.0892
Ruminococcus_bromii dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC -1.57 0.721 0.0295 0.0552 prevalence 1530 429 0.0581 0.0892
Butyrivibrio_crossotus antibiotics Yes antibioticsYes 1.04 0.554 0.0598 0.101 prevalence 1530 43 0.0598 0.0916
Parasutterella_SGB9260 age age age 0.256 0.123 0.0305 0.0902 abundance 1530 269 0.06 0.0918
Parasutterella_SGB9260 age age age -0.127 0.0722 0.0777 0.125 prevalence 1530 269 0.06 0.0918
GGB781_SGB1024 reads reads reads 0.368 0.196 0.0602 0.101 prevalence 1530 18 0.0602 0.0919
Ruminococcus_sp_BSD2780120874_150323_B10 dysbiosis_state dysbiosis_CD dysbiosis_statedysbiosis_CD -3.61 1.92 0.0609 0.102 prevalence 1530 90 0.0609 0.0929
GGB3277_SGB4327 reads reads reads 0.095 0.201 0.0312 0.0918 abundance 1530 152 0.0615 0.0936
GGB3277_SGB4327 reads reads reads 0.127 0.0852 0.137 0.207 prevalence 1530 152 0.0615 0.0936
Bacteroides_caccae reads reads reads -0.243 0.0705 1 1 abundance 1530 958 0.0647 0.0984
Bacteroides_caccae reads reads reads 0.123 0.0578 0.0329 0.061 prevalence 1530 958 0.0647 0.0984
Clostridium_symbiosum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 1.71 0.609 0.033 0.0957 abundance 1530 539 0.0649 0.0985
Clostridium_symbiosum dysbiosis_state dysbiosis_UC dysbiosis_statedysbiosis_UC 0.115 0.329 0.728 0.79 prevalence 1530 539 0.0649 0.0985
Phocaeicola_massiliensis reads reads reads -0.213 0.149 1 1 abundance 1530 396 0.0652 0.0989
Phocaeicola_massiliensis reads reads reads 0.13 0.0608 0.0332 0.0612 prevalence 1530 396 0.0652 0.0989
Eubacterium_siraeum antibiotics Yes antibioticsYes 0.473 0.457 0.233 0.438 abundance 1530 565 0.0654 0.0991
Eubacterium_siraeum antibiotics Yes antibioticsYes 0.414 0.194 0.0333 0.0613 prevalence 1530 565 0.0654 0.0991

Full output file structure

MaAsLin 3 generates two types of output files: data and visualization.

  1. Data output files
    • significant_results.tsv
      • Described above.
    • all_results.tsv
      • Same format as above but for all associations and with an extra column listing any errors from the model fitting.
    • features
      • This folder includes the filtered, normalized, and transformed versions of the input feature table.
      • These steps are performed sequentially in the above order.
      • If an option is set such that a step does not change the data, the resulting table will still be output.
    • models_LM.rds and models_logistic.rds
      • This file contains a list with every model fit object (LM for linear models, logistic for logistic models).
      • It will only be generated if save_models is set to TRUE.
    • residuals_LM.rds and residuals_logstic.rds
      • This file contains a data frame with residuals for each feature.
    • fitted_LM.rds and fitted_logistic.rds
      • This file contains a data frame with fitted values for each feature.
    • ranef_LM.rds and ranef_logistic.rds
      • This file contains a data frame with extracted random effects for each feature (when random effects are specified).
    • maaslin3.log
      • This file contains all log information for the run.
      • It includes all settings, warnings, errors, and steps run.
  2. Visualization output files
    • summary_plot.pdf
      • This file contains a combined coefficient plot and heatmap of the most significant associations. In the heatmap, one star indicates the individual q-value is below the parameter max_significance, and two stars indicate the individual q-value is below max_significance divided by 10.
## [1] TRUE
* association_plots/[metadatum]_[feature]_[association].pdf * A plot is generated for each significant association up to max_pngs. * Scatter plots are used for continuous metadata abundance associations. * Box plots are used for categorical data abundance associations. * Box plots are used for continuous data prevalence associations. * Grids are used for categorical data prevalence associations. * Data points plotted are after filtering, normalization, and transformation so that the scale in the plot is the scale that was used in fitting.
The four types of association plotsThe four types of association plotsThe four types of association plotsThe four types of association plots

The four types of association plots

At the top right of each association plot is the name of the significant association in the results file, the FDR corrected q-value for the individual association, the number of samples in the dataset, and the number of samples with non-zero abundances for the feature. In the plots with categorical metadata variables, the reference category is on the left, and the significant q-values and coefficients in the top right are in the order of the values specified above. Because the displayed coefficients correspond to the full fit model with (possibly) scaled metadata variables, the marginal association plotted might not match the coefficient displayed. However, the plots are intended to provide an interpretable visual while usually agreeing with the full model.

Diagnostics

There are a few common issues to check for in the results:

  1. When warnings or errors are thrown during the fitting process, they are recorded in the error column of all_results.tsv. Often, these indicate model fitting failures or poor fits that should not be trusted, but sometimes the warnings can be benign, and the model fit might still be reasonable. Users should check associations of interest if they produce errors.
  2. Despite the error checking, significant results could still result from poor model fits. These can usually be diagnosed with the visuals in the association_plots directory.
    • Any significant abundance associations with a categorical variable should usually have at least 10 observations in each category.
    • Significant categorical prevalence associations should also have at least 10 samples in which the feature was present and at least 10 samples in which it was absent for each significant category.
    • Significant abundance associations with continuous metadata should be checked visually for influential outliers.

Replotting

Once maaslin3 has been run once, maaslin_plot_results_from_output can be run with the same param_list as the original maaslin3 run to (re-)create the plots. This allows the user to plot the associations even without having the R object returned by maaslin_fit or maaslin3 (e.g., if fitting models through the command line). It is recommended to fit models with simple variables names that are robust to formula plotting and then convert these into proper names for plotting. Likewise, heatmap_vars and coef_plot_vars can be specified in the param_list at any point, but it is usually easier to see how the names come out at first and then choose which metadata variables will go in the coefficient plot and which will go in the heatmap afterwards with maaslin_plot_results_from_output.

# This section is necessary for updating the summary plot and the association plots

# Rename results file with clean titles
all_results <- read.csv('demo_output/all_results.tsv', sep='\t')
all_results <- all_results %>%
  mutate(metadata = case_when(metadata == 'age' ~ 'Age',
                              metadata == 'antibiotics' ~ 'Abx',
                              metadata == 'diagnosis' ~ 'Diagnosis',
                              metadata == 'dysbiosis_state' ~ 'Dysbiosis',
                              metadata == 'reads' ~ 'Read depth'),
         value = case_when(value == 'dysbiosis_CD' ~ 'CD',
                           value == 'dysbiosis_UC' ~ 'UC',
                           value == 'Yes' ~ 'Used', # Antibiotics
                           value == 'age' ~ 'Age',
                           value == 'reads' ~ 'Read depth',
                           TRUE ~ value),
         feature = gsub('_', ' ', feature) %>% 
           gsub(pattern = 'sp ', replacement = 'sp. '))

# Write results
write.table(all_results, 'demo_output/all_results.tsv', sep='\t')

# Set the new heatmap and coefficient plot variables and order them
param_list$heatmap_vars = c('Dysbiosis UC', 'Diagnosis UC', 'Abx Used', 'Age', 'Read depth')
param_list$coef_plot_vars = c('Dysbiosis CD', 'Diagnosis CD')

# This section is necessary for updating the association plots
colnames(param_list$input_data) <- gsub('_', ' ', colnames(param_list$input_data)) %>%
  gsub(pattern = 'sp ', replacement = 'sp. ')

# Rename the features in the norm transformed data file
filtered_data_norm_transformed <- 
  read.csv('demo_output/features/filtered_data_norm_transformed.tsv', sep='\t')
colnames(filtered_data_norm_transformed) <- 
  gsub('_', ' ', colnames(filtered_data_norm_transformed)) %>%
  gsub(pattern = 'sp ', replacement = 'sp. ')
write.table(filtered_data_norm_transformed, 
            'demo_output/features/filtered_data_norm_transformed.tsv', 
            sep='\t', row.names = F)

# Rename the metadata like in the outputs table
colnames(param_list$input_metadata) <- 
  case_when(colnames(param_list$input_metadata) == 'age' ~ 'Age',
            colnames(param_list$input_metadata) == 'antibiotics' ~ 'Abx',
            colnames(param_list$input_metadata) == 'diagnosis' ~ 'Diagnosis',
            colnames(param_list$input_metadata) == 'dysbiosis_state' ~ 'Dysbiosis',
            colnames(param_list$input_metadata) == 'reads' ~ 'Read depth',
            TRUE ~ colnames(param_list$input_metadata))
param_list$input_metadata <- param_list$input_metadata %>%
  mutate(Dysbiosis = case_when(Dysbiosis == 'dysbiosis_UC' ~ 'UC',
                               Dysbiosis == 'dysbiosis_CD' ~ 'CD',
                               Dysbiosis == 'none' ~ 'None') %>%
           factor(levels = c('None', 'UC', 'CD')),
         Abx = case_when(Abx == 'Yes' ~ 'Used',
                         Abx == 'No' ~ 'Not used') %>%
           factor(levels = c('Not used', 'Used')),
         Diagnosis = case_when(Diagnosis == 'nonIBD' ~ 'non-IBD',
                               TRUE ~ Diagnosis) %>%
           factor(levels = c('non-IBD', 'UC', 'CD')))

# Recreate the plots
scatter_plots <- maaslin_plot_results_from_output(param_list)

In the new summary plot below, we can see that the feature names are cleaned up, the metadata names are cleaned up, the set of metadata variables used in the coefficient plot is different, and the metadata used in the heatmap is reordered.

In the association plots, the taxa and metadata have been renamed to be consistent with the results file from earlier.
The four types of association plotsThe four types of association plotsThe four types of association plotsThe four types of association plots

The four types of association plots

4. Advanced Topics

4.1 Interactions

df_input_metadata$CD_dysbiosis = (df_input_metadata$diagnosis == "CD") *
                                 df_input_metadata$dysbiosis
df_input_metadata$UC_dysbiosis = (df_input_metadata$diagnosis == "UC") *
                                 df_input_metadata$dysbiosis

fit_data_ixn = Maaslin2(input_data     = df_input_data, 
                        input_metadata = df_input_metadata, 
                        min_prevalence = 0,
                        normalization  = "NONE",
                        output         = "demo_output_interaction", 
                        fixed_effects  = c("diagnosis", "dysbiosis", "CD_dysbiosis", "UC_dysbiosis"), 
                        reference      = c("diagnosis,nonIBD"))

4.2 Random Effects

Certain studies have a natural “grouping” of sample observations, such as by subject in longitudinal designs or by family in family designs. It is important for statistic analysis to address the non-independence between samples belonging to the same group MaAsLin 3 provides a simple interface for this through the parameter random_effects, where the user can specify the grouping variable to run a mixed effect model instead. For example, we note that HMP2 is a longitudinal design where the same subject (column subject) can have multiple samples. We thus ask MaAsLin 3 to use subject as its random effect grouping variable:

fit_data_random = Maaslin2(input_data     = df_input_data, 
                           input_metadata = df_input_metadata, 
                           min_prevalence = 0,
                           normalization  = "NONE",
                           output         = "demo_output_random", 
                           fixed_effects  = c("diagnosis", "dysbiosis"),
                           random_effects = c("subject"),
                           reference      = c("diagnosis,nonIBD"))

If you are interested in testing the effect of time in a longitudinal study, then the time point variable should be included in fixed_effects during your MaAsLin 3 call.

  • Question: intuitively, can you think of a reason why it is important to address non-independence between samples?
    • Hint: imagine the simple scenario where you have two subject, one case and one control, each has two samples.
    • What is the effective sample size, when samples of the same subject are highly independent, versus when they are highly correlated?

4.3 Additional Options

MaAsLin 3 provide many parameter options for different data pre-processing (normalization, filtering, transfomation) and other tasks. The full list of these options are:

  • min_abundance
    • The minimum abundance for each feature [ Default: 0 ]
  • min_prevalence
    • The minimum percent of samples for which a feature is detected at minimum abundance [ Default: 0.1 ]
  • max_significance
    • The q-value threshold for significance [ Default: 0.25 ]
  • normalization
    • The normalization method to apply [ Default: "TSS" ] [ Choices: "TSS", "CLR", "CSS", "NONE", "TMM" ]
  • transform
    • The transform to apply [ Default: "LOG" ] [ Choices: "LOG", "LOGIT", "AST", "NONE" ]
  • analysis_method
    • The analysis method to apply [ Default: "LM" ] [ Choices: "LM", "CPLM", "ZICP", "NEGBIN", "ZINB" ]
  • correction
    • The correction method for computing the q-value [ Default: "BH" ]
  • standardize
    • Apply z-score so continuous metadata are on the same scale [ Default: TRUE ]
  • plot_heatmap
    • Generate a heatmap for the significant associations [ Default: TRUE ]
  • heatmap_first_n
    • In heatmap, plot top N features with significant associations [ Default: 50 ]
  • plot_scatter
    • Generate scatter plots for the significant associations [ Default: TRUE ]
  • cores
    • The number of R processes to run in parallel [ Default: 1 ]
  • reference
    • The factor to use as a reference for a variable with more than two levels provided as a string of ‘variable,reference’ semi-colon delimited for multiple variables.

4.3.1 Prevalence and abundance filtering in MaAsLin 3

Typically, it only makes sense to test for feature-metadata associations if a feature is non-zero “enough” of the time. “Enough” can vary between studies, but a 10-50% minimum prevalence threshold is not unusual (and up to 70-90% can be reasonable). Since we’re already using a small, selected subset of demo data, we’ll use min_prevalence = 0.1 to test only features with at least 10% non-zero values. Note: this is the default parameter setting in MaAsLin 3.

Similarly, it’s often desirable to test only features that reach a minimum abundance threshold in at least this many samples. By default, MaAsLin 3 will consider any non-zero value to be reliable, and if you’ve already done sufficient QC in your dataset, this is appropriate. However, if you’d like to filter more or be conservative, you can set a minimum abundance threshold like min_abundance = 0.0001 to test only features reaching at least this (relative) abundance.

Putting these arguments together, we can run MaAsLin 3 (and it’ll go even faster!) using both:

fit_data_filter = Maaslin2(input_data     = df_input_data, 
                           input_metadata = df_input_metadata, 
                           normalization  = "NONE",
                           output         = "demo_output_filter", 
                           fixed_effects  = c("diagnosis", "dysbiosis"),
                           reference      = c("diagnosis,nonIBD"),
                           random_effects = c("subject"),
                           min_prevalence = 0.1,
                           min_abundance  = 0.0001)

5. Command Line Interface

MaAsLin 3 can also be run with a command line interface. For example, the demo analysis can be performed with:

Maaslin2.R --transform=AST --fixed_effects="diagnosis,dysbiosis"  /usr/local/lib/R/site-library/Maaslin2/extdata/HMP2_taxonomy.tsv /usr/local/lib/R/site-library/Maaslin2/extdata/HMP2_metadata.tsv demo_output --reference="diagnosis,nonIBD"

Full help documentation:

$ Maaslin2.R --help
Usage: ./R/Maaslin2.R [options] <data.tsv> <metadata.tsv> <output_folder>

Options:
    -h, --help
        Show this help message and exit

    -a MIN_ABUNDANCE, --min_abundance=MIN_ABUNDANCE
        The minimum abundance for each feature [ Default: 0 ]

    -p MIN_PREVALENCE, --min_prevalence=MIN_PREVALENCE
        The minimum percent of samples for which a feature 
        is detected at minimum abundance [ Default: 0.1 ]

    -s MAX_SIGNIFICANCE, --max_significance=MAX_SIGNIFICANCE
        The q-value threshold for significance [ Default: 0.25 ]

    -n NORMALIZATION, --normalization=NORMALIZATION
        The normalization method to apply [ Default: TSS ]
        [ Choices: TSS, CLR, CSS, NONE, TMM ]

    -t TRANSFORM, --transform=TRANSFORM
        The transform to apply [ Default: LOG ]
        [ Choices: LOG, LOGIT, AST, NONE ]

    -m ANALYSIS_METHOD, --analysis_method=ANALYSIS_METHOD
        The analysis method to apply [ Default: LM ]
        [ Choices: LM, CPLM, NEGBIN, ZINB ]

    -r RANDOM_EFFECTS, --random_effects=RANDOM_EFFECTS
        The random effects for the model, comma-delimited
        for multiple effects [ Default: none ]

    -f FIXED_EFFECTS, --fixed_effects=FIXED_EFFECTS
        The fixed effects for the model, comma-delimited
        for multiple effects [ Default: all ]

    -c CORRECTION, --correction=CORRECTION
        The correction method for computing the 
        q-value [ Default: BH ]

    -z STANDARDIZE, --standardize=STANDARDIZE
        Apply z-score so continuous metadata are 
        on the same scale [ Default: TRUE ]

    -l PLOT_HEATMAP, --plot_heatmap=PLOT_HEATMAP
        Generate a heatmap for the significant 
        associations [ Default: TRUE ]

    -i HEATMAP_FIRST_N, --heatmap_first_n=HEATMAP_FIRST_N
        In heatmap, plot top N features with significant 
        associations [ Default: TRUE ]

    -o PLOT_SCATTER, --plot_scatter=PLOT_SCATTER
        Generate scatter plots for the significant
        associations [ Default: TRUE ]

    -e CORES, --cores=CORES
        The number of R processes to run in parallel
        [ Default: 1 ]

    -r REFERENCE, --reference='VARIABLE,REFERENCE'
        The factor to use as a reference for a 
        variable with more than two levels 
        provided as a string of 'variable,reference' 
        semi-colon delimited for multiple variables.